Merge branch 'mliappy_unified' of github.com:Boogie3D/lammps into mliappy_unified

.github/CODEOWNERS

@@ -13,20 +13,21 @@ lib/kim/*             @ellio167
 lib/mesont/*          @iafoss
 
 # whole packages
+src/AMOEBA/*          @sjplimp
 src/COMPRESS/*        @rbberger
 src/GPU/*             @ndtrung81
 src/KOKKOS/*          @stanmoore1
 src/KIM/*             @ellio167
 src/LATTE/*           @cnegre
-src/MESSAGE/*         @sjplimp
 src/MLIAP/*           @athomps
 src/SNAP/*            @athomps
 src/SPIN/*            @julient31
 src/BROWNIAN/*        @samueljmcameron
 src/CG-DNA/*          @ohenrich
-src/CG-SDK/*          @akohlmey
+src/CG-SPICA/*        @yskmiyazaki
 src/COLVARS/*         @giacomofiorin
 src/DIELECTRIC/*      @ndtrung81
+src/ELECTRODE/*       @ludwig-ahrens
 src/FEP/*             @agiliopadua
 src/ML-HDNNP/*        @singraber
 src/INTEL/*           @wmbrownintel

.github/codecov.yml

@@ -7,7 +7,7 @@ coverage:
         threshold: 10%
         only_pulls: false
         branches:
-          - "master"
+          - "develop"
         flags:
           - "unit"
         paths:
@@ -16,14 +16,14 @@ coverage:
     project:
         default:
             branches:
-              - "master"
+              - "develop"
             paths:
               - "src"
             informational: true
     patch:
         default:
             branches:
-              - "master"
+              - "develop"
             paths:
               - "src"
             informational: true

cmake/CMakeLists.txt

@@ -135,13 +135,11 @@ set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
 # ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
 # and prints lots of pointless warnings about "unsafe" functions
 if(MSVC)
-  if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
+  if((CMAKE_CXX_COMPILER_ID STREQUAL "MSVC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Intel"))
     add_compile_options(/Zc:__cplusplus)
     add_compile_options(/wd4244)
     add_compile_options(/wd4267)
-    if(LAMMPS_EXCEPTIONS)
+    add_compile_options(/EHsc)
-      add_compile_options(/EHsc)
-    endif()
   endif()
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()

doc/Makefile

@@ -242,6 +242,6 @@ $(MATHJAX):
 $(ANCHORCHECK): $(VENV)
 	@( \
 		. $(VENV)/bin/activate; \
-		pip install -e utils/converters;\
+		pip $(PIP_OPTIONS) install -e utils/converters;\
 		deactivate;\
 	)

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "23 June 2022" "2022-6-23"
+.TH LAMMPS "1" "3 August 2022" "2022-8-3"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 23 June 2022
+\- Molecular Dynamics Simulator.  Version 3 August 2022
 
 .SH SYNOPSIS
 .B lmp
@@ -161,7 +161,7 @@ list references for specific cite-able features used during a
 run.
 .TP
 \fB\-pk <style> [options]\fR or \fB\-package <style> [options]\fR
-Invoke the \fBpackage\R command with <style> and optional arguments.
+Invoke the \fBpackage\fR command with <style> and optional arguments.
 The syntax is the same as if the command appeared in an input script.
 For example "-pk gpu 2" is the same as "package gpu 2" in the input
 script. The possible styles and options are discussed in the

doc/src/Build_extras.rst

@@ -181,10 +181,10 @@ set appropriate environment variables. Some variables such as
 and the linker to work correctly.
 
 Using CHIP-SPV implementation of HIP is now supported. It allows one to run HIP
-code on Intel GPUs via the OpenCL or Level Zero backends. To use CHIP-SPV, you must 
+code on Intel GPUs via the OpenCL or Level Zero backends. To use CHIP-SPV, you must
-set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake command line as CHIP-SPV does not 
+set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake command line as CHIP-SPV does not
-yet support hipCUB. The use of HIP for Intel GPUs is still experimental so you 
+yet support hipCUB. The use of HIP for Intel GPUs is still experimental so you
-should only use this option in preparations to run on Aurora system at ANL. 
+should only use this option in preparations to run on Aurora system at ANL.
 
 .. code:: bash
 

doc/src/Commands_parse.rst

@@ -123,14 +123,15 @@ LAMMPS:
 .. _six:
 
 6. If you want text with spaces to be treated as a single argument, it
-   can be enclosed in either single or double or triple quotes.  A long
+   can be enclosed in either single (') or double (") or triple (""")
-   single argument enclosed in single or double quotes can span multiple
+   quotes.  A long single argument enclosed in single or double quotes
-   lines if the "&" character is used, as described above.  When the
+   can span multiple lines if the "&" character is used, as described
-   lines are concatenated together (and the "&" characters and line
+   in :ref:`1 <one>` above.  When the lines are concatenated together
-   breaks removed), the text will become a single line.  If you want
+   by LAMMPS (and the "&" characters and line breaks removed), the
-   multiple lines of an argument to retain their line breaks, the text
+   combined text will become a single line.  If you want multiple lines
-   can be enclosed in triple quotes, in which case "&" characters are
+   of an argument to retain their line breaks, the text can be enclosed
-   not needed.  For example:
+   in triple quotes, in which case "&" characters are not needed and do
+   not function as line continuation character.  For example:
 
    .. code-block:: LAMMPS
 
@@ -144,8 +145,9 @@ LAMMPS:
       System temperature = $t
       """
 
-   In each case, the single, double, or triple quotes are removed when
+   In each of these cases, the single, double, or triple quotes are
-   the single argument they enclose is stored internally.
+   removed and the enclosed text stored internally as a single
+   argument.
 
    See the :doc:`dump modify format <dump_modify>`, :doc:`print
    <print>`, :doc:`if <if>`, and :doc:`python <python>` commands for

doc/src/Developer_updating.rst

@@ -23,6 +23,7 @@ Available topics in mostly chronological order are:
 - `Simplify customized error messages`_
 - `Use of "override" instead of "virtual"`_
 - `Simplified and more compact neighbor list requests`_
+- `Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM`_
 
 ----
 
@@ -287,7 +288,7 @@ New:
    comm->forward_comm(this);
    comm->reverse_comm(this);
 
-This change is required or else the code will not compile.
+This change is **required** or else the code will not compile.
 
 Simplified and more compact neighbor list requests
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -321,4 +322,63 @@ New:
    if (cutflag) req->set_cutoff(mycutneigh);
 
 Public access to the ``NeighRequest`` class data members has been
-removed so this update is *required* to avoid compilation failure.
+removed so this update is **required** to avoid compilation failure.
+
+Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: TBD
+
+This change splits the GLOBAL and PERATOM modes of fix STORE into two
+separate fixes STORE/GLOBAL and STORE/PERATOM.  There was very little
+shared code between the two fix STORE modes and the two different code
+paths had to be prefixed with if statements.  Furthermore, some flags
+were used differently in the two modes leading to confusion.  Splitting
+the code into two fix styles, makes it more easily maintainable.  Since
+these are internal fixes, there is no user visible change.
+
+Old:
+
+.. code-block:: C++
+
+   #include "fix_store.h"
+
+   FixStore *fix = dynamic_cast<FixStore *>(
+      modify->add_fix(fmt::format("{} {} STORE peratom 1 13",id_pole,group->names[0]));
+
+   FixStore *fix = dynamic_cast<FixStore *>(modify->get_fix_by_id(id_pole));
+
+New:
+
+.. code-block:: C++
+
+   #include "fix_store_peratom.h"
+
+   FixStorePeratom *fix = dynamic_cast<FixStorePeratom *>(
+      modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 13",id_pole,group->names[0]));
+
+   FixStorePeratom *fix = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_pole));
+
+Old:
+
+.. code-block:: C++
+
+   #include "fix_store.h"
+
+   FixStore *fix = dynamic_cast<FixStore *>(
+      modify->add_fix(fmt::format("{} {} STORE global 1 1",id_fix,group->names[igroup]));
+
+   FixStore *fix = dynamic_cast<FixStore *>(modify->get_fix_by_id(id_fix));
+
+New:
+
+.. code-block:: C++
+
+   #include "fix_store_global.h"
+
+   FixStoreGlobal *fix = dynamic_cast<FixStoreGlobal *>(
+      modify->add_fix(fmt::format("{} {} STORE/GLOBAL 1 1",id_fix,group->names[igroup]));
+
+   FixStoreGlobal *fix = dynamic_cast<FixStoreGlobal *>(modify->get_fix_by_id(id_fix));
+
+This change is **required** or else the code will not compile.

doc/src/Developer_utils.rst

@@ -208,7 +208,7 @@ Argument processing
 Convenience functions
 ^^^^^^^^^^^^^^^^^^^^^
 
-.. doxygenfunction:: logmesg(LAMMPS *lmp, const S &format, Args&&... args)
+.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &format, Args&&... args)
    :project: progguide
 
 .. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)

doc/src/Fortran.rst

@@ -38,11 +38,11 @@ found together with equivalent examples in C and C++ in the
 
 .. note::
 
-   A contributed (and complete!) Fortran interface that more
+   A contributed (and more complete!) Fortran interface that more
-   closely resembles the C-library interface is available
+   closely resembles the C-library interface is available in the
-   in the ``examples/COUPLE/fortran2`` folder.  Please see the
+   ``examples/COUPLE/fortran2`` folder.  Please see the ``README`` file
-   ``README`` file in that folder for more information about it
+   in that folder for more information about it and how to contact its
-   and how to contact its author and maintainer.
+   author and maintainer.
 
 ----------
 
@@ -65,8 +65,9 @@ the optional logical argument set to ``.true.``. Here is a simple example:
 
    PROGRAM testlib
      USE LIBLAMMPS                 ! include the LAMMPS library interface
+     IMPLICIT NONE
      TYPE(lammps)     :: lmp       ! derived type to hold LAMMPS instance
-     CHARACTER(len=*), DIMENSION(*), PARAMETER :: args = &
+     CHARACTER(len=*), PARAMETER :: args(3) = &
          [ CHARACTER(len=12) :: 'liblammps', '-log', 'none' ]
 
      ! create a LAMMPS instance (and initialize MPI)
@@ -78,6 +79,41 @@ the optional logical argument set to ``.true.``. Here is a simple example:
 
    END PROGRAM testlib
 
+It is also possible to pass command line flags from Fortran to C/C++ and
+thus make the resulting executable behave similar to the standalone
+executable (it will ignore the `-in/-i` flag, though).  This allows to
+use the command line to configure accelerator and suffix settings,
+configure screen and logfile output, or to set index style variables
+from the command line and more. Here is a correspondingly adapted
+version of the previous example:
+
+.. code-block:: fortran
+
+   PROGRAM testlib2
+     USE LIBLAMMPS                 ! include the LAMMPS library interface
+     IMPLICIT NONE
+     TYPE(lammps)     :: lmp       ! derived type to hold LAMMPS instance
+     CHARACTER(len=128), ALLOCATABLE :: command_args(:)
+     INTEGER :: i, argc
+
+     ! copy command line flags to `command_args()`
+     argc = COMMAND_ARGUMENT_COUNT()
+     ALLOCATE(command_args(0:argc))
+     DO i=0, argc
+       CALL GET_COMMAND_ARGUMENT(i, command_args(i))
+     END DO
+
+     ! create a LAMMPS instance (and initialize MPI)
+     lmp = lammps(command_args)
+     ! get and print numerical version code
+     PRINT*, 'Program name:   ', command_args(0)
+     PRINT*, 'LAMMPS Version: ', lmp%version()
+     ! delete LAMMPS instance (and shuts down MPI)
+     CALL lmp%close(.TRUE.)
+     DEALLOCATE(command_args)
+
+   END PROGRAM testlib2
+
 --------------------
 
 Executing LAMMPS commands
@@ -102,7 +138,7 @@ Below is a small demonstration of the uses of the different functions:
      USE LIBLAMMPS
      TYPE(lammps)     :: lmp
      CHARACTER(len=512) :: cmds
-     CHARACTER(len=40),ALLOCATABLE :: cmdlist(:)
+     CHARACTER(len=40), ALLOCATABLE :: cmdlist(:)
      CHARACTER(len=10) :: trimmed
      INTEGER :: i
 
@@ -111,10 +147,10 @@ Below is a small demonstration of the uses of the different functions:
      CALL lmp%command('variable zpos index 1.0')
      ! define 10 groups of 10 atoms each
      ALLOCATE(cmdlist(10))
-     DO i=1,10
+     DO i=1, 10
          WRITE(trimmed,'(I10)') 10*i
          WRITE(cmdlist(i),'(A,I1,A,I10,A,A)')       &
-             'group g',i-1,' id ',10*(i-1)+1,':',ADJUSTL(trimmed)
+             'group g', i-1, ' id ', 10*(i-1)+1, ':', ADJUSTL(trimmed)
      END DO
      CALL lmp%commands_list(cmdlist)
      ! run multiple commands from multi-line string
@@ -123,7 +159,7 @@ Below is a small demonstration of the uses of the different functions:
          'create_box 1 box' // NEW_LINE('A') //               &
          'create_atoms 1 single 1.0 1.0 ${zpos}'
      CALL lmp%commands_string(cmds)
-     CALL lmp%close()
+     CALL lmp%close(.TRUE.)
 
    END PROGRAM testcmd
 
@@ -137,9 +173,9 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
 
 .. f:type:: lammps
 
-   Derived type that is the general class of the Fortran interface.
+   Derived type that is the general class of the Fortran interface.  It
-   It holds a reference to the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class instance
+   holds a reference to the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>`
-   that any of the included calls are forwarded to.
+   class instance that any of the included calls are forwarded to.
 
    :f c_ptr handle: reference to the LAMMPS class
    :f close: :f:func:`close`
@@ -202,7 +238,7 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
    This method will call :cpp:func:`lammps_commands_list` to have LAMMPS
    execute a list of input lines.
 
-   :p character(len=*) cmd(*): list of LAMMPS input lines
+   :p character(len=*) cmd(:): list of LAMMPS input lines
 
 .. f:subroutine:: commands_string(str)
 
@@ -210,4 +246,3 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
    execute a block of commands from a string.
 
    :p character(len=*) str: LAMMPS input in string
-

doc/src/Howto_amoeba.rst

@@ -2,9 +2,9 @@ AMOEBA and HIPPO force fields
 =============================
 
 The AMOEBA and HIPPO polarizable force fields were developed by Jay
-Ponder's group at the U Washington at St Louis.  Their implementation
+Ponder's group at the U Washington at St Louis.  The LAMMPS
-in LAMMPS was done using F90 code provided by the Ponder group from
+implementation is based on Fortran 90 code provided by the Ponder
-their `Tinker MD code <https://dasher.wustl.edu/tinker/>`_.
+group in their `Tinker MD software <https://dasher.wustl.edu/tinker/>`_.
 
 The current implementation (July 2022) of AMOEBA in LAMMPS matches the
 version discussed in :ref:`(Ponder) <amoeba-Ponder>`, :ref:`(Ren)

doc/src/Install.rst

@@ -3,10 +3,20 @@ Install LAMMPS
 
 You can download LAMMPS as an executable or as source code.
 
-With source code, you also have to :doc:`build LAMMPS <Build>`.  But you
+When downloading the LAMMPS source code, you also have to :doc:`build
-have more flexibility as to what features to include or exclude in the
+LAMMPS <Build>`.  But you have more flexibility as to what features to
-build.  If you plan to :doc:`modify or extend LAMMPS <Modify>`, then you
+include or exclude in the build.  When you download and install
-need the source code.
+pre-compiled LAMMPS executables, you are limited to install which
+version of LAMMPS is available and which features are included of these
+builds.  If you plan to :doc:`modify or extend LAMMPS <Modify>`, then
+you **must** build LAMMPS from the source code.
+
+.. note::
+
+   If you have questions about the pre-compiled LAMMPS executables, you
+   need to contact the people preparing those executables.  The LAMMPS
+   developers have no control over their choices of how they configure
+   and build their packages and when they update them.
 
 .. toctree::
    :maxdepth: 1

doc/src/Install_conda.rst

@@ -38,3 +38,10 @@ up the Conda capability.
 .. _openkim: https://openkim.org
 .. _conda: https://docs.conda.io/en/latest/index.html
 .. _mini_conda_install: https://docs.conda.io/en/latest/miniconda.html
+
+.. note::
+
+   If you have questions about these pre-compiled LAMMPS executables,
+   you need to contact the people preparing those packages.  The LAMMPS
+   developers have no control over their choices of how they configure
+   and build their packages and when they update them.

doc/src/Install_linux.rst

@@ -3,13 +3,19 @@ Download an executable for Linux
 
 Binaries are available for different versions of Linux:
 
-| :ref:`Pre-built Ubuntu Linux executables <ubuntu>`
+- :ref:`Pre-built Ubuntu Linux executables <ubuntu>`
-| :ref:`Pre-built Fedora Linux executables <fedora>`
+- :ref:`Pre-built Fedora Linux executables <fedora>`
-| :ref:`Pre-built EPEL Linux executables (RHEL, CentOS) <epel>`
+- :ref:`Pre-built EPEL Linux executables (RHEL, CentOS) <epel>`
-| :ref:`Pre-built OpenSuse Linux executables <opensuse>`
+- :ref:`Pre-built OpenSuse Linux executables <opensuse>`
-| :ref:`Gentoo Linux executable <gentoo>`
+- :ref:`Gentoo Linux executable <gentoo>`
-| :ref:`Arch Linux build-script <arch>`
+- :ref:`Arch Linux build-script <arch>`
-|
+
+.. note::
+
+   If you have questions about these pre-compiled LAMMPS executables,
+   you need to contact the people preparing those packages.  The LAMMPS
+   developers have no control over their choices of how they configure
+   and build their packages and when they update them.
 
 ----------
 
@@ -18,41 +24,28 @@ Binaries are available for different versions of Linux:
 Pre-built Ubuntu Linux executables
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-A pre-built LAMMPS executable suitable for running on the latest
+A pre-built LAMMPS executable suitable for running on the latest Ubuntu
-Ubuntu Linux versions, can be downloaded as a Debian package.  This
+Linux versions, can be downloaded as a Debian package.  This allows you
-allows you to install LAMMPS with a single command, and stay
+to install LAMMPS with a single command, and stay (mostly) up-to-date
-up-to-date with the current stable version of LAMMPS by simply updating
+with the current stable version of LAMMPS by simply updating your
-your operating system.  Please note, that the repository below offers
+operating system.
-two LAMMPS packages, ``lammps-daily`` and ``lammps-stable``.  The
-LAMMPS developers recommend to use the ``lammps-stable`` package for
-any production simulations.  The ``lammps-daily`` package is built
-from the LAMMPS development sources, and those versions may have known
-issues and bugs when new features are added and the software has not
-undergone full release testing.
-
-To install the appropriate personal-package archives (PPAs), do the
-following once:
-
-.. code-block:: bash
-
-   $ sudo add-apt-repository ppa:gladky-anton/lammps
-   $ sudo add-apt-repository ppa:openkim/latest
-   $ sudo apt-get update
 
 To install LAMMPS do the following once:
 
 .. code-block:: bash
 
-   $ sudo apt-get install lammps-stable
+   $ sudo apt-get install lammps
 
-This downloads an executable named ``lmp_stable`` to your box, which
+This downloads an executable named ``lmp`` to your box and multiple
-can then be used in the usual way to run input scripts:
+packages with supporting data, examples and libraries as well as any
+missing dependencies.  This executable can then be used in the usual way
+to run input scripts:
 
 .. code-block:: bash
 
-   $ lmp_stable -in in.lj
+   $ lmp -in in.lj
 
-To update LAMMPS to the most current stable version, do the following:
+To update LAMMPS to the latest packaged version, do the following:
 
 .. code-block:: bash
 
@@ -60,44 +53,24 @@ To update LAMMPS to the most current stable version, do the following:
 
 which will also update other packages on your system.
 
-To get a copy of the current documentation and examples:
+The ``lmp`` binary is built with the :ref:`KIM package <kim>` included,
-
+which results in the above command also installing the ``kim-api``
-.. code-block:: bash
+binaries when LAMMPS is installed.  In order to use potentials from
-
+`openkim.org <openkim_>`_, you can also install the ``openkim-models``
-   $ sudo apt-get install lammps-stable-doc
+package
-
-which will download the doc files in
-``/usr/share/doc/lammps-stable-doc/doc`` and example problems in
-``/usr/share/doc/lammps-doc/examples``.
-
-To get a copy of the current potentials files:
-
-.. code-block:: bash
-
-   $ sudo apt-get install lammps-stable-data
-
-which will download the potentials files to
-``/usr/share/lammps-stable/potentials``.  The ``lmp_stable`` binary is
-hard-coded to look for potential files in this directory (it does not
-use the ``LAMMPS_POTENTIALS`` environment variable, as described
-in :doc:`pair_coeff <pair_coeff>` command).
-
-The ``lmp_stable`` binary is built with the :ref:`KIM package <kim>` which
-results in the above command also installing the ``kim-api`` binaries when LAMMPS
-is installed.  In order to use potentials from `openkim.org <openkim_>`_, you
-can install the ``openkim-models`` package
 
 .. code-block:: bash
 
    $ sudo apt-get install openkim-models
 
+Or use the KIM-API commands to download and install individual models.
 To un-install LAMMPS, do the following:
 
 .. code-block:: bash
 
-   $ sudo apt-get remove lammps-stable
+   $ sudo apt-get remove lammps
 
-Please use ``lmp_stable -help`` to see which compilation options, packages,
+Please use ``lmp -help`` to see which compilation options, packages,
 and styles are included in the binary.
 
 Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this
@@ -110,21 +83,21 @@ Ubuntu package capability.
 Pre-built Fedora Linux executables
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Pre-built LAMMPS packages for stable releases are available
+Pre-built LAMMPS packages for stable releases are available in the
-in the Fedora Linux distribution as of version 28. The packages
+Fedora Linux distribution as of Fedora version 28. The packages can be
-can be installed via the dnf package manager. There are 3 basic
+installed via the dnf package manager. There are 3 basic varieties
-varieties (lammps = no MPI, lammps-mpich = MPICH MPI library,
+(lammps = no MPI, lammps-mpich = MPICH MPI library, lammps-openmpi =
-lammps-openmpi = OpenMPI MPI library) and for each support for
+OpenMPI MPI library) and for each support for linking to the C library
-linking to the C library interface (lammps-devel, lammps-mpich-devel,
+interface (lammps-devel, lammps-mpich-devel, lammps-openmpi-devel), the
-lammps-openmpi-devel), the header for compiling programs using
+header for compiling programs using the C library interface
-the C library interface (lammps-headers), and the LAMMPS python
+(lammps-headers), and the LAMMPS python module for Python 3. All
-module for Python 3. All packages can be installed at the same
+packages can be installed at the same time and the name of the LAMMPS
-time and the name of the LAMMPS executable is ``lmp`` and ``lmp_openmpi``
+executable is ``lmp`` and ``lmp_openmpi`` or ``lmp_mpich`` respectively.
-or ``lmp_mpich`` respectively.  By default, ``lmp`` will refer to the
+By default, ``lmp`` will refer to the serial executable, unless one of
-serial executable, unless one of the MPI environment modules is loaded
+the MPI environment modules is loaded (``module load mpi/mpich-x86_64``
-(``module load mpi/mpich-x86_64`` or ``module load mpi/openmpi-x86_64``).
+or ``module load mpi/openmpi-x86_64``).  Then the corresponding parallel
-Then the corresponding parallel LAMMPS executable can be used.
+LAMMPS executable can be used.  The same mechanism applies when loading
-The same mechanism applies when loading the LAMMPS python module.
+the LAMMPS python module.
 
 To install LAMMPS with OpenMPI and run an input ``in.lj`` with 2 CPUs do:
 
@@ -273,3 +246,10 @@ Alternatively, you may use an AUR helper to install these packages.
 
 Note that the AUR provides build-scripts that download the source and
 the build the package on your machine.
+
+.. note::
+
+   It looks like the Arch Linux AUR repository build scripts for LAMMPS
+   have not been updated since the 29 October 2020 version.  You may want
+   to consider installing a more current version of LAMMPS from source
+   directly.

doc/src/Intro_citing.rst

@@ -33,9 +33,9 @@ initial versions of LAMMPS is:
 DOI for the LAMMPS source code
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-LAMMPS developers use the `Zenodo service at CERN <https://zenodo.org/>`_
+The LAMMPS developers use the `Zenodo service at CERN <https://zenodo.org/>`_
-to create digital object identifies (DOI) for stable releases of the
+to create digital object identifiers (DOI) for stable releases of the
-LAMMPS source code. There are two types of DOIs for the LAMMPS source code.
+LAMMPS source code.  There are two types of DOIs for the LAMMPS source code.
 
 The canonical DOI for **all** versions of LAMMPS, which will always
 point to the **latest** stable release version is:

doc/src/Manual.rst

@@ -49,12 +49,12 @@ descriptions of all commands included in the LAMMPS code.
 
 ----------
 
+.. _user_documentation:
 
 ************
 User Guide
 ************
 
-.. _user_documentation:
 .. toctree::
    :maxdepth: 2
    :numbered: 3
@@ -75,11 +75,12 @@ User Guide
    Errors
 
 
+.. _programmer_documentation:
+
 ******************
 Programmer Guide
 ******************
 
-.. _programmer_documentation:
 .. toctree::
    :maxdepth: 2
    :numbered: 3

doc/src/Modify_fix.rst

@@ -23,6 +23,8 @@ derived class.  See fix.h for details.
 +---------------------------+--------------------------------------------------------------------------------------------+
 | init                      | initialization before a run (optional)                                                     |
 +---------------------------+--------------------------------------------------------------------------------------------+
+| init_list                 | store pointer to neighbor list; called by neighbor list code (optional)                    |
++---------------------------+--------------------------------------------------------------------------------------------+
 | setup_pre_exchange        | called before atom exchange in setup (optional)                                            |
 +---------------------------+--------------------------------------------------------------------------------------------+
 | setup_pre_force           | called before force computation in setup (optional)                                        |

doc/src/Packages_details.rst

@@ -157,14 +157,28 @@ AMOEBA package
 
 **Contents:**
 
-TODO
+Implementation of the AMOEBA and HIPPO polarized force fields
+originally developed by Jay Ponder's group at the U Washington at St
+Louis.  The LAMMPS implementation is based on Fortran 90 code
+provided by the Ponder group in their
+`Tinker MD software <https://dasher.wustl.edu/tinker/>`_.
+
+**Authors:** Josh Rackers and Steve Plimpton (Sandia), Trung Nguyen (U
+ Chicago)
 
 **Supporting info:**
 
 * src/AMOEBA: filenames -> commands
 * :doc:`AMOEBA and HIPPO howto <Howto_amoeba>`
+* :doc:`pair_style amoeba <pair_amoeba>`
+* :doc:`pair_style hippo <pair_amoeba>`
+* :doc:`atom_style amoeba <atom_style>`
+* :doc:`angle_style amoeba <angle_amoeba>`
+* :doc:`improper_style amoeba <improper_amoeba>`
+* :doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>`
+* :doc:`fix amoeba/pitorsion <fix_amoeba_pitorsion>`
+* tools/tinker/tinker2lmp.py
 * examples/amoeba
-* TODO
 
 ----------
 
@@ -200,9 +214,10 @@ ATC package
 
 **Contents:**
 
-ATC stands for atoms-to-continuum.  This package implements a :doc:`fix atc <fix_atc>` command to either couple molecular dynamics with
+ATC stands for atoms-to-continuum.  This package implements a
-continuum finite element equations or perform on-the-fly conversion of
+:doc:`fix atc <fix_atc>` command to either couple molecular dynamics
-atomic information to continuum fields.
+with continuum finite element equations or perform on-the-fly
+conversion of atomic information to continuum fields.
 
 **Authors:** Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
 
@@ -317,6 +332,8 @@ models for mesoscale simulations of solids and fracture.  See the
 
 **Authors:** Joel T. Clemmer (Sandia National Labs)
 
+.. versionadded:: 4May2022
+
 **Supporting info:**
 
 * src/BPM filenames -> commands
@@ -845,6 +862,8 @@ groups of atoms that interact with the remaining atoms as electrolyte.
 Ahrens-Iwers (TUHH, Hamburg, Germany), Shern Tee (UQ, Brisbane, Australia) and
 Robert Meissner (TUHH, Hamburg, Germany).
 
+.. versionadded:: 4May2022
+
 **Install:**
 
 This package has :ref:`specific installation instructions <electrode>` on the

doc/src/Run_options.rst

@@ -14,6 +14,7 @@ letter abbreviation can be used:
 * :ref:`-m or -mpicolor <mpicolor>`
 * :ref:`-c or -cite <cite>`
 * :ref:`-nc or -nocite <nocite>`
+* :ref:`-nb or -nonbuf <nonbuf>`
 * :ref:`-pk or -package <package>`
 * :ref:`-p or -partition <partition>`
 * :ref:`-pl or -plog <plog>`
@@ -257,6 +258,24 @@ Disable generating a citation reminder (see above) at all.
 
 ----------
 
+.. _nonbuf:
+
+**-nonbuf**
+
+Turn off buffering for screen and logfile output.  For performance
+reasons, output to the screen and logfile is usually buffered, i.e.
+output is only written to a file if its buffer - typically 4096 bytes -
+has been filled.  When LAMMPS crashes for some reason, however, that can
+mean that there is important output missing.  With this flag the
+buffering can be turned off (only for screen and logfile output) and any
+output will be committed immediately.  Note that when running in
+parallel with MPI, the screen output may still be buffered by the MPI
+library and this cannot be changed by LAMMPS.  This flag should only be
+used for debugging and not for production simulations as the performance
+impact can be significant, especially for large parallel runs.
+
+----------
+
 .. _package:
 
 **-package style args ....**

doc/src/atom_style.rst

@@ -10,7 +10,7 @@ Syntax
 
    atom_style style args
 
-* style = *amoeba* or *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid*
+* style = *amoeba* or *angle* or *atomic* or *body* or *bond* or *charge* or *dielectric* or *dipole* or  *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *mesont* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *wavepacket* or *hybrid*
 
   .. parsed-literal::
 

doc/src/bond_bpm_rotational.rst

@@ -38,8 +38,7 @@ Examples
    bond_style bpm/rotational
    bond_coeff 1 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.02 0.002 0.002
 
-   bond_style bpm/rotational myfix 1000 time id1 id2
+   bond_style bpm/rotational store/local myfix 1000 time id1 id2
-   fix myfix all store/local 1000 3
    dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3]
    dump_modify 1 write_header no
 

doc/src/compute_born_matrix.rst

@@ -33,6 +33,8 @@ Examples
 Description
 """""""""""
 
+.. versionadded:: 4May2022
+
 Define a compute that calculates
 :math:`\frac{\partial{}^2U}{\partial\varepsilon_{i}\partial\varepsilon_{j}}` the
 second derivatives of the potential energy :math:`U` w.r.t. strain

doc/src/compute_chunk_atom.rst

@@ -15,7 +15,7 @@ Syntax
 
   .. parsed-literal::
 
-     style = *bin/1d* or *bin/2d* or *bin/3d* or *bin/sphere* or *type* or *molecule* or c_ID, c_ID[I], f_ID, f_ID[I], v_name
+     style = *bin/1d* or *bin/2d* or *bin/3d* or *bin/sphere* or *bin/cylinder* or *type* or *molecule* or c_ID, c_ID[I], f_ID, f_ID[I], v_name
        *bin/1d* args = dim origin delta
          dim = *x* or *y* or *z*
          origin = *lower* or *center* or *upper* or coordinate value (distance units)
@@ -49,7 +49,7 @@ Syntax
          v_name = per-atom vector calculated by an atom-style variable with name
 
 * zero or more keyword/values pairs may be appended
-* keyword = *region* or *nchunk* or *static* or *compress* or *bound* or *discard* or *pbc* or *units*
+* keyword = *region* or *nchunk* or *limit* or *ids* or *compress* or *discard* or *bound* or *pbc* or *units*
 
   .. parsed-literal::
 
@@ -74,7 +74,7 @@ Syntax
          no = keep atoms with out-of-range chunk IDs by assigning a valid chunk ID
          mixed = keep or discard such atoms according to spatial binning rule
        *bound* values = x/y/z lo hi
-         x/y/z = *x* or *y* or *z* to bound sptial bins in this dimension
+         x/y/z = *x* or *y* or *z* to bound spatial bins in this dimension
          lo = *lower* or coordinate value (distance units)
          hi = *upper* or coordinate value (distance units)
        *pbc* value = *no* or *yes*

doc/src/compute_orientorder_atom.rst

@@ -19,12 +19,12 @@ Syntax
 
   .. parsed-literal::
 
-     keyword = *cutoff* or *nnn* or *degrees* or *components* or *chunksize*
+     keyword = *cutoff* or *nnn* or *degrees* or *wl* or *wl/hat* or *components* or *chunksize*
        *cutoff* value = distance cutoff
        *nnn* value = number of nearest neighbors
        *degrees* values = nlvalues, l1, l2,...
-       *wl* value = yes or no
+       *wl* value = *yes* or *no*
-       *wl/hat* value = yes or no
+       *wl/hat* value = *yes* or *no*
        *components* value = ldegree
        *chunksize* value = number of atoms in each pass
 

doc/src/compute_saed.rst

@@ -41,8 +41,8 @@ Examples
    compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
    compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
 
-   fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
+   fix 1 all saed/vtk 1 1 1 c_1 file Al2O3_001.saed
-   fix saed/vtk 1 1 1 c_2 file Ni_000.saed
+   fix 2 all saed/vtk 1 1 1 c_2 file Ni_000.saed
 
 Description
 """""""""""

doc/src/compute_smd_triangle_vertices.rst

@@ -18,7 +18,7 @@ Examples
 
 .. code-block:: LAMMPS
 
-   compute 1 all smd/triangle/mesh/vertices
+   compute 1 all smd/triangle/vertices
 
 Description
 """""""""""

doc/src/create_atoms.rst

@@ -136,6 +136,8 @@ positions.
             :align: right
             :target: _images/marble_race.jpg
 
+.. versionadded:: 2Jun2022
+
 For the *mesh* style, a file with a triangle mesh in `STL format
 <https://en.wikipedia.org/wiki/STL_(file_format)>`_ is read and one or
 more particles are placed into the area of each triangle.  The reader
@@ -391,6 +393,8 @@ the atom style.  Its value is a prefactor (must be > 0.0, default is
 individual triangles in the triangle mesh that the particle corresponds
 to.
 
+.. versionadded:: 2Jun2022
+
 The *overlap* keyword only applies to the *random* style.  It prevents
 newly created particles from being created closer than the specified
 *Doverlap* distance from any other particle.  When the particles being

doc/src/create_bonds.rst

@@ -10,7 +10,7 @@ Syntax
 
    create_bonds style args ... keyword value ...
 
-* style = *many* or *single/bond* or *single/angle* or *single/dihedral*
+* style = *many* or *single/bond* or *single/angle* or *single/dihedral* or *single/improper*
 
 .. parsed-literal::
 

doc/src/delete_atoms.rst

@@ -55,7 +55,7 @@ Examples
    delete_atoms random fraction 0.1 yes all cube 482793 bond yes
    delete_atoms random fraction 0.3 no polymer NULL 482793 bond yes
    delete_atoms random count 500 no ions NULL 482793
-   detele_atoms variable checkers
+   delete_atoms variable checkers
 
 Description
 """""""""""

doc/src/dihedral_zero.rst

@@ -8,7 +8,10 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   dihedral_style zero [nocoeff]
+   dihedral_style zero keyword
+
+* zero or more keywords may be appended
+* keyword = *nocoeff*
 
 Examples
 """"""""

doc/src/displace_atoms.rst

@@ -36,7 +36,7 @@ Syntax
   .. parsed-literal::
 
        keyword = *units*
-         value = *box* or *lattice*
+         *units* value = *box* or *lattice*
 
 Examples
 """"""""

doc/src/dump.rst

@@ -61,7 +61,7 @@ Syntax
 
 * ID = user-assigned name for the dump
 * group-ID = ID of the group of atoms to be dumped
-* style = *atom* or *atom/gz* or *atom/zstd or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
+* style = *atom* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
 * N = dump every this many timesteps
 * file = name of file to write dump info to
 * args = list of arguments for a particular style
@@ -96,7 +96,7 @@ Syntax
        *xyz/mpiio* args = none
        *yaml* args = same as *custom* args, see below
 
-* *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *netcdf* or *netcdf/mpiio* or *yaml* args = list of atom attributes
+* *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *netcdf* or *netcdf/mpiio* or *yaml* args = list of atom attributes
 
   .. parsed-literal::
 
@@ -414,6 +414,8 @@ from using the (numerical) atom type to an element name (or some
 other label). This will help many visualization programs to guess
 bonds and colors.
 
+.. versionadded:: 4May2022
+
 Dump style *yaml* has the same command syntax as style *custom* and
 writes YAML format files that can be easily parsed by a variety of data
 processing tools and programming languages.  Each timestep will be

doc/src/dump_h5md.rst

@@ -6,31 +6,31 @@ dump h5md command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    dump ID group-ID h5md N file.h5 args
 
 * ID = user-assigned name for the dump
 * group-ID = ID of the group of atoms to be imaged
-* h5md = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
+* *h5md* = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
 * N = dump every this many timesteps
 * file.h5 = name of file to write to
+* args = *position* options or *image* or *velocity* options or *force* options or *species* options or *file_from* ID or *box* value or *create_group* value or *author* value = list of data elements to dump, with their dump "sub-intervals"
 
-.. parsed-literal::
+  .. parsed-literal::
 
-   args = list of data elements to dump, with their dump "sub-intervals"
+     *position* options
-     position options
+     *image*
-     image
+     *velocity* options
-     velocity options
+     *force* options
-     force options
+     *species* options
-     species options
+     *file_from* ID = do not open a new file, re-use the already opened file from dump ID
-     file_from ID: do not open a new file, re-use the already opened file from dump ID
+     *box* value = *yes* or *no*
-     box value = *yes* or *no*
+     *create_group* value = *yes* or *no*
-     create_group value = *yes* or *no*
+     *author* value = quoted string
-     author value = quoted string
 
-Note that at least one element must be specified and image may only be
+Note that at least one element must be specified and that *image* may only be
-present if position is specified first.
+present if *position* is specified first.
 
 For the elements *position*, *velocity*, *force* and *species*, a
 sub-interval may be specified to write the data only every N_element
@@ -39,7 +39,7 @@ specified by this option directly following the element declaration:
 
 .. parsed-literal::
 
-   every N_element
+         options = *every* N_element
 
 Examples
 """"""""

doc/src/dump_image.rst

@@ -56,7 +56,7 @@ Syntax
          phi = azimuthal view angle (degrees)
          theta or phi can be a variable (see below)
        *center* values = flag Cx Cy Cz = center point of image
-         flag = "s" for static, "d" for dynamic
+         flag = *s* for static, *d* for dynamic
          Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
          Cx,Cy,Cz can be variables (see below)
        *up* values = Ux Uy Uz = direction that is "up" in image
@@ -110,13 +110,13 @@ Syntax
        *amap* args = lo hi style delta N entry1 entry2 ... entryN
          lo = number or *min* = lower bound of range of color map
          hi = number or *max* = upper bound of range of color map
-         style = 2 letters = "c" or "d" or "s" plus "a" or "f"
+         style = 2 letters = *c* or *d* or *s* plus *a* or *f*
-           "c" for continuous
+           *c* for continuous
-           "d" for discrete
+           *d* for discrete
-           "s" for sequential
+           *s* for sequential
-           "a" for absolute
+           *a* for absolute
-           "f" for fractional
+           *f* for fractional
-         delta = binsize (only used for style "s", otherwise ignored)
+         delta = binsize (only used for style *s*, otherwise ignored)
            binsize = range is divided into bins of this width
          N = # of subsequent entries
          entry = value color (for continuous style)

doc/src/dump_modify.rst

@@ -380,6 +380,8 @@ performed with dump style *xtc*\ .
 
 ----------
 
+.. versionadded:: 4May2022
+
 The *colname* keyword can be used to change the default header keyword
 for dump styles: *atom*, *custom*, and *cfg* and their compressed, ADIOS,
 and MPIIO variants.  The setting for *ID string* replaces the default

doc/src/fix_ave_chunk.rst

@@ -17,12 +17,12 @@ Syntax
 * Nfreq = calculate averages every this many timesteps
 * chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
 * one or more input values can be listed
-* value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name
+* value = vx, vy, vz, fx, fy, fz, density/mass, density/number, mass, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name
 
   .. parsed-literal::
 
-       vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
+       vx,vy,vz,fx,fy,fz,mass = atom attribute (velocity, force component, mass)
-       density/number, density/mass = number or mass density
+       density/number, density/mass = number or mass density (per volume)
        temp = temperature
        c_ID = per-atom vector calculated by a compute with ID
        c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
@@ -99,29 +99,33 @@ averages can be used by other :doc:`output commands <Howto_output>` such
 as :doc:`thermo_style custom <thermo_style>`, and can also be written to
 a file.
 
-In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute
-to a single chunk (or no chunk).  The ID for this command is specified
+chunk/atom <compute_chunk_atom>` command, which assigns each atom to a
-as chunkID.  For example, a single chunk could be the atoms in a
+single chunk (or no chunk).  The ID for this command is specified as
-molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` page and the :doc:`Howto chunk <Howto_chunk>` page for details of how chunks can be
+chunkID.  For example, a single chunk could be the atoms in a molecule
-defined and examples of how they can be used to measure properties of
+or atoms in a spatial bin.  See the :doc:`compute chunk/atom
-a system.
+<compute_chunk_atom>` page and the :doc:`Howto chunk <Howto_chunk>`
+page for details of how chunks can be defined and examples of how they
+can be used to measure properties of a system.
 
 Note that only atoms in the specified group contribute to the summing
-and averaging calculations.  The :doc:`compute chunk/atom <compute_chunk_atom>` command defines its own group as
+and averaging calculations.  The :doc:`compute chunk/atom
-well as an optional region.  Atoms will have a chunk ID = 0, meaning
+<compute_chunk_atom>` command defines its own group as well as an
-they belong to no chunk, if they are not in that group or region.
+optional region.  Atoms will have a chunk ID = 0, meaning they belong
-Thus you can specify the "all" group for this command if you simply
+to no chunk, if they are not in that group or region.  Thus you can
-want to use the chunk definitions provided by chunkID.
+specify the "all" group for this command if you simply want to use the
+chunk definitions provided by chunkID.
 
 Each specified per-atom value can be an atom attribute (position,
-velocity, force component), a mass or number density, or the result of
+velocity, force component), a number or mass density, a mass or
-a :doc:`compute <compute>` or :doc:`fix <fix>` or the evaluation of an
+temperature, or the result of a :doc:`compute <compute>` or :doc:`fix
-atom-style :doc:`variable <variable>`.  In the latter cases, the
+<fix>` or the evaluation of an atom-style :doc:`variable <variable>`.
-compute, fix, or variable must produce a per-atom quantity, not a
+In the latter cases, the compute, fix, or variable must produce a
-global quantity.  Note that the :doc:`compute property/atom <compute_property_atom>` command provides access to
+per-atom quantity, not a global quantity.  Note that the :doc:`compute
-any attribute defined and stored by atoms.  If you wish to
+property/atom <compute_property_atom>` command provides access to any
-time-average global quantities from a compute, fix, or variable, then
+attribute defined and stored by atoms.  If you wish to time-average
-see the :doc:`fix ave/time <fix_ave_time>` command.
+global quantities from a compute, fix, or variable, then see the
+:doc:`fix ave/time <fix_ave_time>` command.
 
 The per-atom values of each input vector are summed and averaged
 independently of the per-atom values in other input vectors.
@@ -145,8 +149,9 @@ means all indices from m to n (inclusive).
 
 Using a wildcard is the same as if the individual columns of the array
 had been listed one by one.  E.g. these 2 fix ave/chunk commands are
-equivalent, since the :doc:`compute property/atom <compute_property_atom>` command creates, in this
+equivalent, since the :doc:`compute property/atom
-case, a per-atom array with 3 columns:
+<compute_property_atom>` command creates, in this case, a per-atom
+array with 3 columns:
 
 .. code-block:: LAMMPS
 
@@ -194,28 +199,31 @@ discussed below.
 .. note::
 
    To perform per-chunk averaging within a *Nfreq* time window, the
-   number of chunks *Nchunk* defined by the :doc:`compute chunk/atom <compute_chunk_atom>` command must remain constant.  If
+   number of chunks *Nchunk* defined by the :doc:`compute chunk/atom
-   the *ave* keyword is set to *running* or *window* then *Nchunk* must
+   <compute_chunk_atom>` command must remain constant.  If the *ave*
-   remain constant for the duration of the simulation.  This fix forces
+   keyword is set to *running* or *window* then *Nchunk* must remain
-   the chunk/atom compute specified by chunkID to hold *Nchunk* constant
+   constant for the duration of the simulation.  This fix forces the
-   for the appropriate time windows, by not allowing it to re-calculate
+   chunk/atom compute specified by chunkID to hold *Nchunk* constant
-   *Nchunk*, which can also affect how it assigns chunk IDs to atoms.
+   for the appropriate time windows, by not allowing it to
-   This is particularly important to understand if the chunks defined by
+   re-calculate *Nchunk*, which can also affect how it assigns chunk
-   the :doc:`compute chunk/atom <compute_chunk_atom>` command are spatial
+   IDs to atoms.  This is particularly important to understand if the
-   bins.  If its *units* keyword is set to *box* or *lattice*, then the
+   chunks defined by the :doc:`compute chunk/atom
-   number of bins *Nchunk* and size of each bin will be fixed over the
+   <compute_chunk_atom>` command are spatial bins.  If its *units*
-   *Nfreq* time window, which can affect which atoms are discarded if the
+   keyword is set to *box* or *lattice*, then the number of bins
+   *Nchunk* and size of each bin will be fixed over the *Nfreq* time
+   window, which can affect which atoms are discarded if the
    simulation box size changes.  If its *units* keyword is set to
-   *reduced*, then the number of bins *Nchunk* will still be fixed, but
+   *reduced*, then the number of bins *Nchunk* will still be fixed,
-   the size of each bin can vary at each timestep if the simulation box
+   but the size of each bin can vary at each timestep if the
-   size changes, e.g. for an NPT simulation.
+   simulation box size changes, e.g. for an NPT simulation.
 
 ----------
 
-The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
+The atom attribute values (vx,vy,vz,fx,fy,fz,mass) are
-As noted above, any other atom attributes can be used as input values
+self-explanatory.  As noted above, any other atom attributes can be
-to this fix by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying
+used as input values to this fix by using the :doc:`compute
-an input value from that compute.
+property/atom <compute_property_atom>` command and then specifying an
+input value from that compute.
 
 The *density/number* value means the number density is computed for
 each chunk, i.e. number/volume.  The *density/mass* value means the
@@ -243,12 +251,13 @@ Note that currently this temperature only includes translational
 degrees of freedom for each atom.  No rotational degrees of freedom
 are included for finite-size particles.  Also no degrees of freedom
 are subtracted for any velocity bias or constraints that are applied,
-such as :doc:`compute temp/partial <compute_temp_partial>`, or :doc:`fix shake <fix_shake>` or :doc:`fix rigid <fix_rigid>`.  This is because
+such as :doc:`compute temp/partial <compute_temp_partial>`, or
-those degrees of freedom (e.g. a constrained bond) could apply to sets
+:doc:`fix shake <fix_shake>` or :doc:`fix rigid <fix_rigid>`.  This is
-of atoms that are both included and excluded from a specific chunk,
+because those degrees of freedom (e.g. a constrained bond) could apply
-and hence the concept is somewhat ill-defined.  In some cases, you can
+to sets of atoms that are both included and excluded from a specific
-use the *adof* and *cdof* keywords to adjust the calculated degrees of
+chunk, and hence the concept is somewhat ill-defined.  In some cases,
-freedom appropriately, as explained below.
+you can use the *adof* and *cdof* keywords to adjust the calculated
+degrees of freedom appropriately, as explained below.
 
 Also note that a bias can be subtracted from atom velocities before
 they are used in the above formula for KE, by using the *bias*
@@ -256,22 +265,22 @@ keyword.  This allows, for example, a thermal temperature to be
 computed after removal of a flow velocity profile.
 
 Note that the per-chunk temperature calculated by this fix and the
-:doc:`compute temp/chunk <compute_temp_chunk>` command can be different.
+:doc:`compute temp/chunk <compute_temp_chunk>` command can be
-The compute calculates the temperature for each chunk for a single
+different.  The compute calculates the temperature for each chunk for
-snapshot.  This fix can do that but can also time average those values
+a single snapshot.  This fix can do that but can also time average
-over many snapshots, or it can compute a temperature as if the atoms
+those values over many snapshots, or it can compute a temperature as
-in the chunk on different timesteps were collected together as one set
+if the atoms in the chunk on different timesteps were collected
-of atoms to calculate their temperature.  The compute allows the
+together as one set of atoms to calculate their temperature.  The
-center-of-mass velocity of each chunk to be subtracted before
+compute allows the center-of-mass velocity of each chunk to be
-calculating the temperature; this fix does not.
+subtracted before calculating the temperature; this fix does not.
 
 If a value begins with "c\_", a compute ID must follow which has been
 previously defined in the input script.  If no bracketed integer is
 appended, the per-atom vector calculated by the compute is used.  If a
 bracketed integer is appended, the Ith column of the per-atom array
 calculated by the compute is used.  Users can also write code for
-their own compute styles and :doc:`add them to LAMMPS <Modify>`.
+their own compute styles and :doc:`add them to LAMMPS <Modify>`.  See
-See the discussion above for how I can be specified with a wildcard
+the discussion above for how I can be specified with a wildcard
 asterisk to effectively specify multiple values.
 
 If a value begins with "f\_", a fix ID must follow which has been
@@ -307,9 +316,10 @@ atoms in the chunk.  The averaged output value for the chunk on the
 average over atoms across the entire *Nfreq* timescale.  For the
 *density/number* and *density/mass* values, the volume (bin volume or
 system volume) used in the final normalization will be the volume at
-the final *Nfreq* timestep. For the *temp* values, degrees of freedom and
+the final *Nfreq* timestep. For the *temp* values, degrees of freedom
-kinetic energy are summed separately across the entire *Nfreq* timescale, and
+and kinetic energy are summed separately across the entire *Nfreq*
-the output value is calculated by dividing those two sums.
+timescale, and the output value is calculated by dividing those two
+sums.
 
 If the *norm* setting is *sample*, the chunk value is summed over
 atoms for each sample, as is the count, and an "average sample value"
@@ -431,44 +441,50 @@ the first of each section of output.  In the third line the values are
 replaced with the appropriate value names, e.g. fx or c_myCompute[2].
 
 The words in parenthesis only appear with corresponding columns if the
-chunk style specified for the :doc:`compute chunk/atom <compute_chunk_atom>` command supports them.  The OrigID
+chunk style specified for the :doc:`compute chunk/atom
-column is only used if the *compress* keyword was set to *yes* for the
+<compute_chunk_atom>` command supports them.  The OrigID column is
-:doc:`compute chunk/atom <compute_chunk_atom>` command.  This means that
+only used if the *compress* keyword was set to *yes* for the
-the original chunk IDs (e.g. molecule IDs) will have been compressed
+:doc:`compute chunk/atom <compute_chunk_atom>` command.  This means
-to remove chunk IDs with no atoms assigned to them.  Thus a compressed
+that the original chunk IDs (e.g. molecule IDs) will have been
-chunk ID of 3 may correspond to an original chunk ID or molecule ID of
+compressed to remove chunk IDs with no atoms assigned to them.  Thus a
+compressed chunk ID of 3 may correspond to an original chunk ID or
+molecule ID of
 415.  The OrigID column will list 415 for the third chunk.
 
 The CoordN columns only appear if a *binning* style was used in the
 :doc:`compute chunk/atom <compute_chunk_atom>` command.  For *bin/1d*,
 *bin/2d*, and *bin/3d* styles the column values are the center point
 of the bin in the corresponding dimension.  Just Coord1 is used for
-*bin/1d*, Coord2 is added for *bin/2d*, Coord3 is added for *bin/3d*\ .
+*bin/1d*, Coord2 is added for *bin/2d*, Coord3 is added for *bin/3d*\
-For *bin/sphere*, just Coord1 is used, and it is the radial
+.  For *bin/sphere*, just Coord1 is used, and it is the radial
 coordinate.  For *bin/cylinder*, Coord1 and Coord2 are used.  Coord1
 is the radial coordinate (away from the cylinder axis), and coord2 is
 the coordinate along the cylinder axis.
 
-Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command <compute_chunk_atom>` is *box* or *lattice*, the
+Note that if the value of the *units* keyword used in the
-coordinate values will be in distance :doc:`units <units>`.  If the
+:doc:`compute chunk/atom command <compute_chunk_atom>` is *box* or
-value of the *units* keyword is *reduced*, the coordinate values will
+*lattice*, the coordinate values will be in distance :doc:`units
-be in unitless reduced units (0-1).  This is not true for the Coord1 value
+<units>`.  If the value of the *units* keyword is *reduced*, the
-of style *bin/sphere* or *bin/cylinder* which both represent radial
+coordinate values will be in unitless reduced units (0-1).  This is
-dimensions.  Those values are always in distance :doc:`units <units>`.
+not true for the Coord1 value of style *bin/sphere* or *bin/cylinder*
+which both represent radial dimensions.  Those values are always in
+distance :doc:`units <units>`.
 
 ----------
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to :doc:`binary restart files
-are relevant to this fix.
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
+relevant to this fix.
 
 This fix computes a global array of values which can be accessed by
 various :doc:`output commands <Howto_output>`.  The values can only be
 accessed on timesteps that are multiples of *Nfreq* since that is when
 averaging is performed.  The global array has # of rows = the number
-of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The # of columns =
+of chunks *Nchunk* as calculated by the specified :doc:`compute
+chunk/atom <compute_chunk_atom>` command.  The # of columns =
 M+1+Nvalues, where M = 1 to 4, depending on whether the optional
 columns for OrigID and CoordN are used, as explained above.  Following
 the optional columns, the next column contains the count of atoms in
@@ -483,7 +499,8 @@ since they are typically already normalized by the count of atoms in
 each chunk.
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_ave_time.rst

@@ -277,6 +277,8 @@ is the length of the input vectors, and the number of columns is the
 number of values.  Thus the file ends up to be a series of these array
 sections.
 
+.. versionadded:: 4May2022
+
 If the filename ends in '.yaml' or '.yml' then the output format
 conforms to the `YAML standard <https://yaml.org/>`_ which allows
 easy import that data into tools and scripts that support reading YAML
@@ -329,6 +331,8 @@ appropriate fields from the fix ave/time command.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
+.. versionadded:: 4May2022
+
 No information about this fix is written to :doc:`binary restart files
 <restart>`.  The :doc:`fix_modify colname <fix_modify>` option can be
 used to change the name of the column in the output file.  When writing

doc/src/fix_electrode_conp.rst

@@ -25,38 +25,47 @@ Syntax
 
 .. parsed-literal::
 
-   fix ID group-ID electrode/conp potential eta keyword values ...
+   fix ID group-ID style args keyword value ...
-   fix ID group-ID electrode/conq charge eta keyword values ...
-   fix ID group-ID electrode/thermo potential eta temp T_v tau_v rng_v keyword values ...
 
-* ID, group-ID are documented in fix command
+* ID, group-ID are documented in :doc:`fix <fix>` command
-* mode = electrode/conp or electrode/conq or electrode/thermo
+* style = *electrode/conp* or *electrode/conq* or *electrode/thermo*
-* potential = electrode potential
+* args = arguments used by a particular style
-* charge = electrode charge
+
-* eta = reciprocal width of electrode charge smearing
+  .. parsed-literal::
-* T_v = temperature of thermo-potentiostat
+
-* tau_v = time constant of thermo-potentiostat
+       *electrode/conp* args = potential eta
-* rng_v = integer used to initialize random number generator
+       *electrode/conq* args = charge eta
+       *electrode/thermo* args = potential eta *temp* values
+            potential = electrode potential
+            charge = electrode charge
+            eta = reciprocal width of electrode charge smearing
+            *temp* values = T_v tau_v rng_v
+                T_v = temperature of thermo-potentiostat
+                tau_v = time constant of thermo-potentiostat
+                rng_v = integer used to initialize random number generator
+
+* zero or more keyword/value pairs may be appended
+* keyword = *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv*
 
 .. parsed-literal::
 
-    *symm(etry) on/off*
+    *symm* value = *on* or *off*
         turn on/off charge neutrality constraint for the electrodes
-    *couple group-ID value*
+    *couple* values = group-ID val
         group-ID = group of atoms treated as additional electrode
-        value = electric potential or charge on this electrode
+        val = electric potential or charge on this electrode
-    *etypes values = atom types*
+    *etypes* values = type
-        specify atom types exclusive to the electrode for optimized neighbor lists
+        type = atom type (can be a range) exclusive to the electrode for optimized neighbor lists
-    *ffield on/off*
+    *ffield* value = *on* or *off*
         turn on/off finite-field implementation
-    *write_mat filename*
+    *write_mat* value = filename
-        write elastance matrix to file
+        filename = file to which to write elastance matrix
-    *write_inv filename*
+    *write_inv* value = filename
-        write inverted matrix to file
+        filename = file to which to write inverted matrix
-    *read_mat filename*
+    *read_mat* value = filename
-        read elastance matrix from file
+        filename = file from which to read elastance matrix
-    *read_inv filename*
+    *read_inv* value = filename
-        read inverted matrix from file
+        filename = file from which to read inverted matrix
 
 Examples
 """"""""

doc/src/fix_flow_gauss.rst

@@ -24,9 +24,9 @@ Syntax
 
   .. parsed-literal::
 
-       *energy* value = no or yes
+       *energy* value = *no* or *yes*
-         no = do not compute work done by this fix
+         *no* = do not compute work done by this fix
-         yes = compute work done by this fix
+         *yes* = compute work done by this fix
 
 Examples
 """"""""

doc/src/fix_ipi.rst

@@ -14,8 +14,14 @@ Syntax
 * ipi = style name of this fix command
 * address = internet address (FQDN or IP), or UNIX socket name
 * port = port number (ignored for UNIX sockets)
-* optional keyword = *unix*, if present uses a unix socket
+
-* optional keyword = *reset*, if present reset electrostatics at each call
+* zero or more keywords may be appended
+* keyword = *unix* or *reset*
+
+  .. parsed-literal::
+
+       *unix* args = none = use a unix socket
+       *reset* args = none = reset electrostatics at each call
 
 Examples
 """"""""

doc/src/fix_nh_uef.rst

@@ -22,13 +22,14 @@ Syntax
 
   .. parsed-literal::
 
-     keyword = *ext* or *strain* or *iso* or *x* or *y* or *z* or *tchain* or *pchain* or *tloop* or *ploop* or *mtk*
+     keyword = *erate* or *ext* or *strain* or *temp* or *iso* or *x* or *y* or *z* or *tchain* or *pchain* or *tloop* or *ploop* or *mtk*
+       *erate* values = e_x e_y = engineering strain rates (required)
        *ext* value = *x* or *y* or *z* or *xy* or *yz* or *xz* = external dimensions
          sets the external dimensions used to calculate the scalar pressure
        *strain* values = e_x e_y = initial strain
          usually not needed, but may be needed to resume a run with a data file.
-       *iso*, *x*, *y*, *z*, *tchain*, *pchain*, *tloop*, *ploop*, *mtk* keywords
+       *temp*, *iso*, *x*, *y*, *z*, *tchain*, *pchain*, *tloop*, *ploop*, *mtk*
-         documented by the :doc:`fix npt <fix_nh>` command
+         keywords documented by the :doc:`fix npt <fix_nh>` command
 
 Examples
 """"""""

doc/src/fix_npt_sphere.rst

@@ -22,7 +22,7 @@ Syntax
 
      *disc* value = none = treat particles as 2d discs, not spheres
 
-* additional thermostat and barostat related keyword/value pairs from the :doc:`fix npt <fix_nh>` command can be appended
+* NOTE: additional thermostat and barostat and dipole related keyword/value pairs from the :doc:`fix npt <fix_nh>` command can be appended
 
 Examples
 """"""""
@@ -33,6 +33,7 @@ Examples
    fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
    fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 disc
    fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
+   fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 update dipole
    fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial
 
 Description
@@ -61,8 +62,9 @@ The only difference between discs and spheres in this context is their
 moment of inertia, as used in the time integration.
 
 Additional parameters affecting the thermostat and barostat are
-specified by keywords and values documented with the :doc:`fix npt <fix_nh>` command.  See, for example, discussion of the *temp*,
+specified by keywords and values documented with the :doc:`fix npt
-*iso*, *aniso*, and *dilate* keywords.
+<fix_nh>` command.  See, for example, discussion of the *temp*, *iso*,
+*aniso*, and *dilate* keywords.
 
 The particles in the fix group are the only ones whose velocities and
 positions are updated by the velocity/position update portion of the
@@ -87,8 +89,10 @@ this, the fix creates its own computes of style "temp/sphere" and
    compute fix-ID_temp all temp/sphere
    compute fix-ID_press all pressure fix-ID_temp
 
-See the :doc:`compute temp/sphere <compute_temp_sphere>` and :doc:`compute pressure <compute_pressure>` commands for details.  Note that the
+See the :doc:`compute temp/sphere <compute_temp_sphere>` and
-IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+:doc:`compute pressure <compute_pressure>` commands for details.  Note
+that the IDs of the new computes are the fix-ID + underscore + "temp"
+or fix_ID
 + underscore + "press", and the group for the new computes is "all"
 since pressure is computed for the entire system.
 
@@ -170,7 +174,9 @@ defined by the :doc:`dimension <dimension>` keyword.
 Related commands
 """"""""""""""""
 
-:doc:`fix npt <fix_nh>`, :doc:`fix nve_sphere <fix_nve_sphere>`, :doc:`fix nvt_sphere <fix_nvt_sphere>`, :doc:`fix npt_asphere <fix_npt_asphere>`, :doc:`fix_modify <fix_modify>`
+:doc:`fix npt <fix_nh>`, :doc:`fix nve_sphere <fix_nve_sphere>`,
+     :doc:`fix nvt_sphere <fix_nvt_sphere>`, :doc:`fix npt_asphere
+     <fix_npt_asphere>`, :doc:`fix_modify <fix_modify>`
 
 Default
 """""""

doc/src/fix_nve_sphere.rst

@@ -51,7 +51,8 @@ If the *update* keyword is used with the *dipole* value, then the
 orientation of the dipole moment of each particle is also updated
 during the time integration.  This option should be used for models
 where a dipole moment is assigned to finite-size particles,
-e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole <atom_style>` command.
+e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole
+<atom_style>` command.
 
 The default dipole orientation integrator can be changed to the
 Dullweber-Leimkuhler-McLachlan integration scheme
@@ -75,11 +76,13 @@ moment of inertia, as used in the time integration.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to :doc:`binary restart files
-are relevant to this fix.  No global or per-atom quantities are stored
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
-by this fix for access by various :doc:`output commands <Howto_output>`.
+relevant to this fix.  No global or per-atom quantities are stored by
+this fix for access by various :doc:`output commands <Howto_output>`.
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_nvt_sphere.rst

@@ -22,7 +22,7 @@ Syntax
 
        *disc* value = none = treat particles as 2d discs, not spheres
 
-* additional thermostat related keyword/value pairs from the :doc:`fix nvt <fix_nh>` command can be appended
+* NOTE: additional thermostat and dipole related keyword/value pairs from the :doc:`fix nvt <fix_nh>` command can be appended
 
 Examples
 """"""""
@@ -32,6 +32,7 @@ Examples
    fix 1 all nvt/sphere temp 300.0 300.0 100.0
    fix 1 all nvt/sphere temp 300.0 300.0 100.0 disc
    fix 1 all nvt/sphere temp 300.0 300.0 100.0 drag 0.2
+   fix 1 all nvt/sphere temp 300.0 300.0 100.0 update dipole
 
 Description
 """""""""""
@@ -77,13 +78,13 @@ underscore + "temp", and the group for the new compute is the same as
 the fix group.
 
 Note that this is NOT the compute used by thermodynamic output (see
-the :doc:`thermo_style <thermo_style>` command) with ID = *thermo_temp*.
+the :doc:`thermo_style <thermo_style>` command) with ID =
-This means you can change the attributes of this fix's temperature
+*thermo_temp*.  This means you can change the attributes of this fix's
-(e.g. its degrees-of-freedom) via the
+temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify
-:doc:`compute_modify <compute_modify>` command or print this temperature
+<compute_modify>` command or print this temperature during
-during thermodynamic output via the :doc:`thermo_style custom <thermo_style>` command using the appropriate compute-ID.
+thermodynamic output via the :doc:`thermo_style custom <thermo_style>`
-It also means that changing attributes of *thermo_temp* will have no
+command using the appropriate compute-ID.  It also means that changing
-effect on this fix.
+attributes of *thermo_temp* will have no effect on this fix.
 
 Like other fixes that perform thermostatting, this fix can be used
 with :doc:`compute commands <compute>` that remove a "bias" from the
@@ -148,7 +149,9 @@ defined by the :doc:`dimension <dimension>` keyword.
 Related commands
 """"""""""""""""
 
-:doc:`fix nvt <fix_nh>`, :doc:`fix nve_sphere <fix_nve_sphere>`, :doc:`fix nvt_asphere <fix_nvt_asphere>`, :doc:`fix npt_sphere <fix_npt_sphere>`, :doc:`fix_modify <fix_modify>`
+:doc:`fix nvt <fix_nh>`, :doc:`fix nve_sphere <fix_nve_sphere>`,
+     :doc:`fix nvt_asphere <fix_nvt_asphere>`, :doc:`fix npt_sphere
+     <fix_npt_sphere>`, :doc:`fix_modify <fix_modify>`
 
 Default
 """""""

doc/src/fix_oneway.rst

@@ -21,9 +21,9 @@ Examples
 
 .. code-block:: LAMMPS
 
-   fix ions oneway 10 semi -x
+   fix 1 ions oneway 10 semi -x
-   fix all oneway 1 left -z
+   fix 2 all oneway 1 left -z
-   fix all oneway 1 right z
+   fix 3 all oneway 1 right z
 
 Description
 """""""""""

doc/src/fix_property_atom.rst

@@ -15,18 +15,18 @@ Syntax
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * property/atom = style name of this fix command
-* name1,name2,... = *mol* or *q* or *rmass* or *i_name* or *d_name* or *i2_name* or *d2_name*
+* name1,name2,... = *mol* or *q* or *rmass* or i_name or d_name or i2_name or d2_name
 
   .. parsed-literal::
 
        *mol* = molecule IDs
        *q* = charge
        *rmass* = per-atom mass
-       *i_name* = new integer vector referenced by name
+       i_name = new integer vector referenced by name
-       *d_name* = new floating-point vector referenced by name
+       d_name = new floating-point vector referenced by name
-       *i2_name* = new integer array referenced by name
+       i2_name = new integer array referenced by name
           i2_name arg = N = number of columns in the array
-       *d2_name* = new floating-point array referenced by name
+       d2_name = new floating-point array referenced by name
           d2_name arg = N = number of columns in the array
 
 * zero of more keyword/value pairs may be appended

doc/src/fix_rigid.rst

@@ -88,7 +88,7 @@ Syntax
          Tstart,Tstop = desired temperature at start/stop of run (temperature units)
          Tdamp = temperature damping parameter (time units)
          seed = random number seed to use for white noise (positive integer)
-       *reinit* = *yes* or *no*
+       *reinit* value = *yes* or *no*
        *temp* values = Tstart Tstop Tdamp
          Tstart,Tstop = desired temperature at start/stop of run (temperature units)
          Tdamp = temperature damping parameter (time units)
@@ -98,7 +98,7 @@ Syntax
        *x* or *y* or *z* values = Pstart Pstop Pdamp
          Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
          Pdamp = stress damping parameter (time units)
-       *couple* = *none* or *xyz* or *xy* or *yz* or *xz*
+       *couple* value = *none* or *xyz* or *xy* or *yz* or *xz*
        *tparam* values = Tchain Titer Torder
          Tchain = length of Nose/Hoover thermostat chain
          Titer = number of thermostat iterations performed

doc/src/group2ndx.rst

@@ -1,4 +1,5 @@
 .. index:: group2ndx
+.. index:: ndx2group
 
 group2ndx command
 =================

doc/src/if.rst

@@ -25,7 +25,7 @@ Examples
 
    if "${steps} > 1000" then quit
    if "${myString} == a10" then quit
-   if "$x <= $y" then "print X is smaller = $x" else "print Y is smaller = $y"
+   if "$x <= $y" then "print 'X is smaller = $x'" else "print 'Y is smaller = $y'"
    if "(${eng} > 0.0) || ($n < 1000)" then &
      "timestep 0.005" &
    elif $n<10000 &

doc/src/improper_hybrid.rst

@@ -17,7 +17,7 @@ Examples
 
 .. code-block:: LAMMPS
 
-   improper_style hybrid harmonic helix
+   improper_style hybrid harmonic cvff
    improper_coeff 1 harmonic 120.0 30
    improper_coeff 2 cvff 20.0 -1 2
 

doc/src/label.rst

@@ -38,7 +38,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-none
+:doc:`jump <jump>`, :doc:`next <next>`
 
 
 Default

doc/src/neigh_modify.rst

@@ -22,24 +22,24 @@ Syntax
        *check* value = *yes* or *no*
          *yes* = only build if some atom has moved half the skin distance or more
          *no* = always build on 1st step that *every* and *delay* are satisfied
-       *once*
+       *once* value = *yes* or *no*
          *yes* = only build neighbor list once at start of run and never rebuild
          *no* = rebuild neighbor list according to other settings
-       *cluster*
+       *cluster* value = *yes* or *no*
          *yes* = check bond,angle,etc neighbor list for nearby clusters
          *no* = do not check bond,angle,etc neighbor list for nearby clusters
        *include* value = group-ID
          group-ID = only build pair neighbor lists for atoms in this group
        *exclude* values:
-         type M N
+         *type* M N
            M,N = exclude if one atom in pair is type M, other is type N
-         group group1-ID group2-ID
+         *group* group1-ID group2-ID
            group1-ID,group2-ID = exclude if one atom is in 1st group, other in 2nd
-         molecule/intra group-ID
+         *molecule/intra* group-ID
            group-ID = exclude if both atoms are in the same molecule and in group
-         molecule/inter group-ID
+         *molecule/inter* group-ID
            group-ID = exclude if both atoms are in different molecules and in group
-         none
+         *none*
            delete all exclude settings
        *page* value = N
          N = number of pairs stored in a single neighbor page

doc/src/package.rst

@@ -18,16 +18,16 @@ Syntax
        *gpu* args = Ngpu keyword value ...
          Ngpu = # of GPUs per node
          zero or more keyword/value pairs may be appended
-         keywords = *neigh* or *newton* or *pair/only* or *binsize* or *split* or *gpuID* or *tpa* or *blocksize* or *platform* or *device_type* or *ocl_args*
+         keywords = *neigh* or *newton* or *pair/only* or *binsize* or *split* or *gpuID* or *tpa* or *blocksize* or *omp* or *platform* or *device_type* or *ocl_args*
            *neigh* value = *yes* or *no*
-             yes = neighbor list build on GPU (default)
+             *yes* = neighbor list build on GPU (default)
-             no = neighbor list build on CPU
+             *no* = neighbor list build on CPU
            *newton* = *off* or *on*
-             off = set Newton pairwise flag off (default and required)
+             *off* = set Newton pairwise flag off (default and required)
-             on = set Newton pairwise flag on (currently not allowed)
+             *on* = set Newton pairwise flag on (currently not allowed)
            *pair/only* = *off* or *on*
-             off = apply "gpu" suffix to all available styles in the GPU package (default)
+             *off* = apply "gpu" suffix to all available styles in the GPU package (default)
-             on  = apply "gpu" suffix only pair styles
+             *on* = apply "gpu" suffix only pair styles
            *binsize* value = size
              size = bin size for neighbor list construction (distance units)
            *split* = fraction
@@ -42,7 +42,7 @@ Syntax
              id = For OpenCL, platform ID for the GPU or accelerator
            *gpuID* values = id
              id = ID of first GPU to be used on each node
-           *device_type* value = *intelgpu* or *nvidiagpu* or *amdgpu* or *applegpu* or *generic* or *custom,val1,val2,...*
+           *device_type* value = *intelgpu* or *nvidiagpu* or *amdgpu* or *applegpu* or *generic* or *custom*,val1,val2,...
              val1,val2,... = custom OpenCL accelerator configuration parameters (see below for details)
            *ocl_args* value = args
              args = List of additional OpenCL compiler arguments delimited by colons
@@ -57,13 +57,13 @@ Syntax
            *omp* value = Nthreads
              Nthreads = number of OpenMP threads to use on CPU (default = 0)
            *lrt* value = *yes* or *no*
-             yes = use additional thread dedicated for some PPPM calculations
+             *yes* = use additional thread dedicated for some PPPM calculations
-             no = do not dedicate an extra thread for some PPPM calculations
+             *no* = do not dedicate an extra thread for some PPPM calculations
            *balance* value = split
              split = fraction of work to offload to co-processor, -1 for dynamic
            *ghost* value = *yes* or *no*
-             yes = include ghost atoms for offload
+             *yes* = include ghost atoms for offload
-             no = do not include ghost atoms for offload
+             *no* = do not include ghost atoms for offload
            *tpc* value = Ntpc
              Ntpc = max number of co-processor threads per co-processor core (default = 4)
            *tptask* value = Ntptask
@@ -71,7 +71,7 @@ Syntax
            *no_affinity* values = none
        *kokkos* args = keyword value ...
          zero or more keyword/value pairs may be appended
-         keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* *comm/pair/forward* *comm/fix/forward* or *comm/reverse* or *comm/pair/reverse* or *gpu/aware* or *pair/only*
+         keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *neigh/transpose* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* or *comm/pair/forward* or *comm/fix/forward* or *comm/reverse* or *comm/pair/reverse* or *gpu/aware* or *pair/only*
            *neigh* value = *full* or *half*
              full = full neighbor list
              half = half neighbor list built in thread-safe manner
@@ -79,14 +79,14 @@ Syntax
              full = full neighbor list
              half = half neighbor list built in thread-safe manner
            *neigh/thread* value = *off* or *on*
-             off = thread only over atoms
+             *off* = thread only over atoms
-             on = thread over both atoms and neighbors
+             *on* = thread over both atoms and neighbors
            *neigh/transpose* value = *off* or *on*
-             off = use same memory layout for GPU neigh list build as pair style
+             *off* = use same memory layout for GPU neigh list build as pair style
-             on = use transposed memory layout for GPU neigh list build
+             *on* = use transposed memory layout for GPU neigh list build
            *newton* = *off* or *on*
-             off = set Newton pairwise and bonded flags off
+             *off* = set Newton pairwise and bonded flags off
-             on = set Newton pairwise and bonded flags on
+             *on* = set Newton pairwise and bonded flags on
            *binsize* value = size
              size = bin size for neighbor list construction (distance units)
            *comm* value = *no* or *host* or *device*
@@ -96,23 +96,25 @@ Syntax
            *comm/pair/forward* value = *no* or *device*
            *comm/fix/forward* value = *no* or *device*
            *comm/reverse* value = *no* or *host* or *device*
+             *no* = perform communication pack/unpack in non-KOKKOS mode
+             *host* = perform pack/unpack on host (e.g. with OpenMP threading)
+             *device* = perform pack/unpack on device (e.g. on GPU)
            *comm/pair/reverse* value = *no* or *device*
-             no = perform communication pack/unpack in non-KOKKOS mode
+             *no* = perform communication pack/unpack in non-KOKKOS mode
-             host = perform pack/unpack on host (e.g. with OpenMP threading)
+             *device* = perform pack/unpack on device (e.g. on GPU)
-             device = perform pack/unpack on device (e.g. on GPU)
            *gpu/aware* = *off* or *on*
-             off = do not use GPU-aware MPI
+             *off* = do not use GPU-aware MPI
-             on = use GPU-aware MPI (default)
+             *on* = use GPU-aware MPI (default)
            *pair/only* = *off* or *on*
-             off = use device acceleration (e.g. GPU) for all available styles in the KOKKOS package (default)
+             *off* = use device acceleration (e.g. GPU) for all available styles in the KOKKOS package (default)
-             on  = use device acceleration only for pair styles (and host acceleration for others)
+             *on*  = use device acceleration only for pair styles (and host acceleration for others)
        *omp* args = Nthreads keyword value ...
          Nthreads = # of OpenMP threads to associate with each MPI process
          zero or more keyword/value pairs may be appended
          keywords = *neigh*
            *neigh* value = *yes* or *no*
-             yes = threaded neighbor list build (default)
+             *yes* = threaded neighbor list build (default)
-             no = non-threaded neighbor list build
+             *no* = non-threaded neighbor list build
 
 Examples
 """"""""

doc/src/pair_brownian.rst

@@ -36,7 +36,7 @@ Examples
 
 .. code-block:: LAMMPS
 
-   pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1)
+   pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 # (assuming radius = 1)
    pair_coeff 1 1 2.05 2.8
    pair_coeff * *
 

doc/src/pair_coeff.rst

@@ -24,7 +24,7 @@ Examples
    pair_coeff * * 1.0 1.0
    pair_coeff * * nialhjea 1 1 2
    pair_coeff * 3 morse.table ENTRY1
-   pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid)
+   pair_coeff 1 2 lj/cut 1.0 1.0 2.5 # (for pair_style hybrid)
 
 Description
 """""""""""

doc/src/pair_dipole.rst

@@ -78,12 +78,12 @@ Examples
 Description
 """""""""""
 
-Style *lj/cut/dipole/cut* computes interactions between pairs of particles
+Style *lj/cut/dipole/cut* computes interactions between pairs of
-that each have a charge and/or a point dipole moment.  In addition to
+particles that each have a charge and/or a point dipole moment.  In
-the usual Lennard-Jones interaction between the particles (Elj) the
+addition to the usual Lennard-Jones interaction between the particles
-charge-charge (Eqq), charge-dipole (Eqp), and dipole-dipole (Epp)
+(Elj) the charge-charge (Eqq), charge-dipole (Eqp), and dipole-dipole
-interactions are computed by these formulas for the energy (E), force
+(Epp) interactions are computed by these formulas for the energy (E),
-(F), and torque (T) between particles I and J.
+force (F), and torque (T) between particles I and J.
 
 .. math::
 
@@ -112,18 +112,18 @@ interactions are computed by these formulas for the energy (E), force
                       \frac{3}{r^5} (\vec{p_i} \bullet \vec{r})
                       (\vec{p_j} \times \vec{r})
 
-where :math:`q_i` and :math:`q_j` are the charges on the two particles,
+where :math:`q_i` and :math:`q_j` are the charges on the two
-:math:`\vec{p_i}` and :math:`\vec{p_j}` are the dipole moment vectors of
+particles, :math:`\vec{p_i}` and :math:`\vec{p_j}` are the dipole
-the two particles, r is their separation distance, and the vector r =
+moment vectors of the two particles, r is their separation distance,
-Ri - Rj is the separation vector between the two particles.  Note that
+and the vector r = Ri - Rj is the separation vector between the two
-Eqq and Fqq are simply Coulombic energy and force, Fij = -Fji as
+particles.  Note that Eqq and Fqq are simply Coulombic energy and
-symmetric forces, and Tij != -Tji since the torques do not act
+force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
-symmetrically.  These formulas are discussed in :ref:`(Allen) <Allen2>`
+torques do not act symmetrically.  These formulas are discussed in
-and in :ref:`(Toukmaji) <Toukmaji2>`.
+:ref:`(Allen) <Allen2>` and in :ref:`(Toukmaji) <Toukmaji2>`.
 
 Also note, that in the code, all of these terms (except Elj) have a
-:math:`C/\epsilon` prefactor, the same as the Coulombic term in the LJ +
+:math:`C/\epsilon` prefactor, the same as the Coulombic term in the
-Coulombic pair styles discussed :doc:`here <pair_lj>`.  C is an
+LJ + Coulombic pair styles discussed :doc:`here <pair_lj>`.  C is an
 energy-conversion constant and epsilon is the dielectric constant
 which can be set by the :doc:`dielectric <dielectric>` command.  The
 same is true of the equations that follow for other dipole pair
@@ -135,11 +135,11 @@ moment. In general, a shifted-force potential is a (slightly) modified
 potential containing extra terms that make both the energy and its
 derivative go to zero at the cutoff distance; this removes
 (cutoff-related) problems in energy conservation and any numerical
-instability in the equations of motion :ref:`(Allen) <Allen2>`. Shifted-force
+instability in the equations of motion :ref:`(Allen)
-interactions for the Lennard-Jones (E_LJ), charge-charge (Eqq),
+<Allen2>`. Shifted-force interactions for the Lennard-Jones (E_LJ),
-charge-dipole (Eqp), dipole-charge (Epq) and dipole-dipole (Epp)
+charge-charge (Eqq), charge-dipole (Eqp), dipole-charge (Epq) and
-potentials are computed by these formulas for the energy (E), force
+dipole-dipole (Epp) potentials are computed by these formulas for the
-(F), and torque (T) between particles I and J:
+energy (E), force (F), and torque (T) between particles I and J:
 
 .. math::
 
@@ -207,65 +207,52 @@ potentials are computed by these formulas for the energy (E), force
 where :math:`\epsilon` and :math:`\sigma` are the standard LJ
 parameters, :math:`r_c` is the cutoff, :math:`q_i` and :math:`q_j` are
 the charges on the two particles, :math:`\vec{p_i}` and
-:math:`\vec{p_j}` are the dipole moment vectors of the two particles, r
+:math:`\vec{p_j}` are the dipole moment vectors of the two particles,
-is their separation distance, and the vector r = Ri - Rj is the
+r is their separation distance, and the vector r = Ri - Rj is the
-separation vector between the two particles.  Note that Eqq and Fqq are
+separation vector between the two particles.  Note that Eqq and Fqq
-simply Coulombic energy and force, Fij = -Fji as symmetric forces, and
+are simply Coulombic energy and force, Fij = -Fji as symmetric forces,
-Tij != -Tji since the torques do not act symmetrically.  The
+and Tij != -Tji since the torques do not act symmetrically.  The
 shifted-force formula for the Lennard-Jones potential is reported in
 :ref:`(Stoddard) <Stoddard>`.  The original (non-shifted) formulas for
 the electrostatic potentials, forces and torques can be found in
-:ref:`(Price) <Price2>`. The shifted-force electrostatic potentials have
+:ref:`(Price) <Price2>`. The shifted-force electrostatic potentials
-been obtained by applying equation 5.13 of :ref:`(Allen) <Allen2>`. The
+have been obtained by applying equation 5.13 of :ref:`(Allen)
-formulas for the corresponding forces and torques have been obtained by
+<Allen2>`. The formulas for the corresponding forces and torques have
-applying the 'chain rule' as in appendix C.3 of :ref:`(Allen) <Allen2>`.
+been obtained by applying the 'chain rule' as in appendix C.3 of
+:ref:`(Allen) <Allen2>`.
 
 If one cutoff is specified in the pair_style command, it is used for
 both the LJ and Coulombic (q,p) terms.  If two cutoffs are specified,
 they are used as cutoffs for the LJ and Coulombic (q,p) terms
-respectively. This pair style also supports an optional *scale* keyword
+respectively. This pair style also supports an optional *scale*
-as part of a pair_coeff statement, where the interactions can be
+keyword as part of a pair_coeff statement, where the interactions can
-scaled according to this factor. This scale factor is also made available
+be scaled according to this factor. This scale factor is also made
-for use with fix adapt.
+available for use with fix adapt.
 
-Style *lj/cut/dipole/long* computes long-range point-dipole
+Style *lj/cut/dipole/long* computes the short-range portion of
-interactions as discussed in :ref:`(Toukmaji) <Toukmaji2>`. Dipole-dipole,
+point-dipole interactions as discussed in :ref:`(Toukmaji)
-dipole-charge, and charge-charge interactions are all supported, along
+<Toukmaji2>`. Dipole-dipole, dipole-charge, and charge-charge
-with the standard 12/6 Lennard-Jones interactions, which are computed
+interactions are all supported, along with the standard 12/6
-with a cutoff.  A :doc:`kspace_style <kspace_style>` must be defined to
+Lennard-Jones interactions, which are computed with a cutoff.  A
-use this pair style.  Currently, only :doc:`kspace_style ewald/disp <kspace_style>` support long-range point-dipole
+:doc:`kspace_style <kspace_style>` must be defined to use this pair
-interactions.
+style.  If only dipoles (not point charges) are included in the model,
+the kspace style can be one of these 3 options, all of which compute
+the long-range portion of dipole-dipole interactions.  If the model
+includes point charges (in addition to dipoles), then only the first
+of these kspace styles can be used:
 
-Style *lj/long/dipole/long* also computes point-dipole interactions as
+* :doc:`kspace_style ewald/disp <kspace_style>`
-discussed in :ref:`(Toukmaji) <Toukmaji2>`. Long-range dipole-dipole,
+* :doc:`kspace_style ewald/dipole <kspace_style>`
-dipole-charge, and charge-charge interactions are all supported, along
+* :doc:`kspace_style pppm/dipole <kspace_style>`
-with the standard 12/6 Lennard-Jones interactions.  LJ interactions
-can be cutoff or long-ranged.
 
-For style *lj/long/dipole/long*, if *flag_lj* is set to *long*, no
+Style *lj/long/dipole/long* has the same functionality as style
-cutoff is used on the LJ 1/r\^6 dispersion term.  The long-range
+*lj/cut/dipole/long*, except it also has an option to compute 12/6
-portion is calculated by using the :doc:`kspace_style ewald_disp <kspace_style>` command.  The specified LJ cutoff then
+Lennard-Jones interactions for use with a long-range dispersion kspace
-determines which portion of the LJ interactions are computed directly
+style.  This is done by setting its *flag_lj* argument to *long*.  For
-by the pair potential versus which part is computed in reciprocal
+long-range LJ interactions, the doc:`kspace_style ewald/disp
-space via the Kspace style.  If *flag_lj* is set to *cut*, the LJ
+<kspace_style>` command must be used.
-interactions are simply cutoff, as with :doc:`pair_style lj/cut <pair_lj>`.  If *flag_lj* is set to *off*, LJ interactions
-are not computed at all.
 
-If *flag_coul* is set to *long*, no cutoff is used on the Coulombic or
+----------
-dipole interactions.  The long-range portion is calculated by using
-*ewald_disp* of the :doc:`kspace_style <kspace_style>` command. If
-*flag_coul* is set to *off*, Coulombic and dipole interactions are not
-computed at all.
-
-Atoms with dipole moments should be integrated using the :doc:`fix nve/sphere update dipole <fix_nve_sphere>` or the :doc:`fix nvt/sphere update dipole <fix_nvt_sphere>` command to rotate the
-dipole moments.  The *omega* option on the :doc:`fix langevin <fix_langevin>` command can be used to thermostat the
-rotational motion.  The :doc:`compute temp/sphere <compute_temp_sphere>`
-command can be used to monitor the temperature, since it includes
-rotational degrees of freedom.  The :doc:`atom_style hybrid dipole sphere <atom_style>` command should be used since
-it defines the point dipoles and their rotational state.
-The magnitude and orientation of the dipole moment for each particle
-can be defined by the :doc:`set <set>` command or in the "Atoms" section
-of the data file read in by the :doc:`read_data <read_data>` command.
 
 The following coefficients must be defined for each pair of atoms
 types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@@ -287,6 +274,40 @@ type pair.
 
 ----------
 
+Note that for systems using these pair styles, typically particles
+should be able to exert torque on each other via their dipole moments
+so that the particle and its dipole moment can rotate.  This requires
+they not be point particles, but finite-size spheres.  Thus you should
+use a command like :doc:`atom_style hybrid sphere dipole <atom_style>`
+to use particles with both attributes.
+
+The magnitude and orientation of the dipole moment for each particle
+can be defined by the :doc:`set <set>` command or in the "Atoms"
+section of the data file read in by the :doc:`read_data <read_data>`
+command.
+
+Rotating finite-size particles have 6 degrees of freedom (DOFs),
+translation and rotational.  You can use the :doc:`compute temp/sphere
+<compute_temp_sphere>` command to monitor a temperature which includes
+all these DOFs.
+
+Finite-size particles with dipole moments should be integrated using
+one of these options:
+
+* :doc:`fix nve/sphere update dipole <fix_nve_sphere>`
+* :doc:`fix nve/sphere update dipole <fix_nve_sphere>` plus :doc:`fix langevin omega yes <fix_langevin>`
+* :doc:`fix nvt/sphere update dipole <fix_nvt_sphere>`
+* :doc:`fix npt/sphere update dipole <fix_npt_sphere>`
+
+In all cases the "update dipole" setting insures the dipole moments
+are also rotated when the finite-size spheres rotate.  The 2nd and 3rd
+bullets perform thermostatting; in the case of a Langevin thermostat
+the "omega yes" option also thermostats the rotational degrees of
+freedom (if desired).  The 4th bullet performs thermostatting and
+barostatting.
+
+----------
+
 .. include:: accel_styles.rst
 
 ----------

doc/src/pair_rann.rst

@@ -17,8 +17,8 @@ Examples
 .. code-block:: LAMMPS
 
     pair_style rann
-    pair_coeff ** Mg.rann Mg
+    pair_coeff * * Mg.rann Mg
-    pair_coeff ** MgAlalloy.rann Mg Mg Al Mg
+    pair_coeff * * MgAlalloy.rann Mg Mg Al Mg
 
 Description
 """""""""""

doc/src/pair_smatb.rst

@@ -14,13 +14,9 @@ Syntax
 
    pair_style style args
 
-* style = *smatb*
+* style = *smatb* or *smatb/single*
 * args = none
 
-.. parsed-literal::
-
-     *smatb*
-
 Examples
 """"""""
 
@@ -29,13 +25,18 @@ Examples
    pair_style smatb
    pair_coeff 1 1 2.88 10.35 4.178 0.210 1.818 4.07293506 4.9883063257983666
 
+   pair_style smatb/single
+   pair_coeff 1 1 2.88 10.35 4.178 0.210 1.818 4.07293506 4.9883063257983666
+
 
 Description
 """""""""""
 
-The *smatb* styles compute the Second Moment Approximation to the Tight Binding
+.. versionadded:: 4May2022
-:ref:`(Cyrot) <Cyrot>`, :ref:`(Gupta) <Gupta>`, :ref:`(Rosato) <Rosato>`,
+
-given by
+The *smatb* and *smatb/single* styles compute the Second Moment
+Approximation to the Tight Binding :ref:`(Cyrot) <Cyrot>`,
+:ref:`(Gupta) <Gupta>`, :ref:`(Rosato) <Rosato>`, given by
 
 .. math::
       E_{i}  = \sum_{j,R_{ij}\leq R_{c}} \alpha(R_{ij}) - \sqrt{\sum_{j,R_{ij}\leq R_{c}}\Xi^2(R_{ij})}
@@ -66,6 +67,8 @@ exponential terms and their first and second derivatives are smoothly
 reduced to zero, from the inner cutoff :math:`R_{sc}` to the outer
 cutoff :math:`R_{c}`.
 
+The *smatb/single* style is an optimization when using only a single atom type.
+
 Coefficients
 """"""""""""
 
@@ -100,10 +103,10 @@ For atom type pairs I,J and I != J the coefficients are not automatically mixed.
 Restrictions
 """"""""""""
 
-This pair style is part of the SMTBQ package and is only enabled
+These pair styles are part of the SMTBQ package and are only enabled
 if LAMMPS is built with that package.  See the :doc:`Build package <Build_package>` page for more info.
 
-These pair potentials require the :doc:`newton <newton>` setting to be "on" for pair interactions.
+These pair styles require the :doc:`newton <newton>` setting to be "on" for pair interactions.
 
 Related commands
 """"""""""""""""

doc/src/pair_sw.rst

@@ -75,6 +75,8 @@ where :math:`\phi_2` is a two-body term and :math:`\phi_3` is a
 three-body term.  The summations in the formula are over all neighbors J
 and K of atom I within a cutoff distance :math:`a `\sigma`.
 
+.. versionadded:: 14Dec2021
+
 The *sw/mod* style is designed for simulations of materials when
 distinguishing three-body angles are necessary, such as borophene and
 transition metal dichalcogenides, which cannot be described by the

doc/src/pair_sw_angle_table.rst

@@ -31,6 +31,8 @@ Used in example input script:
 Description
 """""""""""
 
+.. versionadded:: 2Jun2022
+
 The *sw/angle/table* style is a modification of the original
 :doc:`pair_style sw <pair_sw>`. It has been developed for coarse-grained
 simulations (of water) (:ref:`Scherer1 <Scherer1>`), but can be employed

doc/src/pair_threebody_table.rst

@@ -35,6 +35,8 @@ Used in example input scripts:
 Description
 """""""""""
 
+.. versionadded:: 2Jun2022
+
 The *threebody/table* style is a pair style for generic tabulated
 three-body interactions.  It has been developed for (coarse-grained)
 simulations (of water) with Kernel-based machine learning (ML)

doc/src/pair_wf_cut.rst

@@ -84,8 +84,8 @@ little to be gained by choosing other values of :math:`\nu` and
 This pair style does not support the :doc:`pair_modify <pair_modify>`
 mixing and table options.
 
-The :doc:`pair_modify <pair_modify>` tail option is not relevant
+The :doc:`pair_modify <pair_modify>` tail and shift options are not
-for this pair style as it goes to zero at the cut-off radius.
+relevant for this pair style as it goes to zero at the cut-off radius.
 
 This pair style writes its information to :doc:`binary restart files
 <restart>`, so pair_style and pair_coeff commands do not need to be

doc/src/thermo_modify.rst

@@ -11,7 +11,7 @@ Syntax
    thermo_modify keyword value ...
 
 * one or more keyword/value pairs may be listed
-* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *format* or *temp* or *press*
+* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *colname* or *format* or *temp* or *press*
 
   .. parsed-literal::
 
@@ -153,6 +153,8 @@ containing the timestep and CPU time ("multi"), or in a YAML format
 block ("yaml").  This modify option overrides the *one*, *multi*, or
 *yaml* thermo_style settings.
 
+.. versionadded:: 4May2022
+
 The *colname* keyword can be used to change the default header keyword
 for a column or field of thermodynamic output.  The setting for *ID
 string* replaces the default text with the provided string.  *ID* can be

doc/src/variable.rst

@@ -66,7 +66,7 @@ Syntax
                            bound(group,dir,region), gyration(group,region), ke(group,reigon),
                            angmom(group,dim,region), torque(group,dim,region),
                            inertia(group,dimdim,region), omega(group,dim,region)
-         special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), extract_setting(name)
+         special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name)
          feature functions = is_active(category,feature), is_available(category,feature), is_defined(category,id)
          atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
          atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
@@ -939,6 +939,20 @@ The is_file(name) function is a test whether *name* is a (readable) file
 and returns 1 in this case, otherwise it returns 0.  For that *name*
 is taken as a literal string and must not have any blanks in it.
 
+The is_os(name) function is a test whether *name* is part of the OS
+information that LAMMPS collects and provides in the
+:cpp:func:`platform::os_info() <LAMMPS_NS::platform::os_info>` function.
+The argument *name* is interpreted as a regular expression as documented
+for the :cpp:func:`utils::strmatch() <LAMMPS_NS::utils::strmatch>`
+function. This allows to adapt LAMMPS inputs to the OS it runs on:
+
+.. code-block:: LAMMPS
+
+   if $(is_os(^Windows)) then &
+     "shell copy ${input_dir}\some_file.txt ." &
+   else &
+     "shell cp ${input_dir}/some_file.txt ."
+
 The extract_setting(name) function enables access to basic settings for
 the LAMMPS executable and the running simulation via calling the
 :cpp:func:`lammps_extract_setting` library function.  For example, the
@@ -1002,7 +1016,7 @@ step
 
 .. code-block:: LAMMPS
 
-   timestep $(2.0*(1.0+2.0*is_active(pair,respa))
+   timestep $(2.0*(1.0+2.0*is_active(pair,respa)))
    if $(is_active(pair,respa)) then "run_style respa 4 3 2 2  improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2  improper 1 pair 2 kspace 3"
 
 The *is_available(category,name)* function allows to query whether

doc/utils/sphinx-config/_static/css/lammps.css

@@ -39,6 +39,18 @@ hr {
      display: none;
 }
 
+#userdoc.toctree-wrapper.compound p {
+     display: none;
+}
+
+#progdoc.toctree-wrapper.compound p {
+     display: none;
+}
+
+#reference.toctree-wrapper.compound p {
+     display: none;
+}
+
 .ui.tabular.menu .item {
     padding-right: 1em;
     padding-left: 1em;

doc/utils/sphinx-config/_themes/lammps_theme/.gitignore

@@ -0,0 +1 @@
+!*.html

doc/utils/sphinx-config/_themes/lammps_theme/search.html

@@ -4,17 +4,8 @@
 {% endblock %}
 {% block body %}
   <div id="search-results">
-<script>
+    <script async src="https://cse.google.com/cse.js?cx=000956471495417073164:5ggs_m6ymw0">
-  (function() {
+    </script>
-    var cx = '012685039201307511604:um7if1hinba';
+    <div class="gcse-search"></div>
-    var gcse = document.createElement('script');
-    gcse.type = 'text/javascript';
-    gcse.async = true;
-    gcse.src = 'https://cse.google.com/cse.js?cx=' + cx;
-    var s = document.getElementsByTagName('script')[0];
-    s.parentNode.insertBefore(gcse, s);
-  })();
-</script>
-<gcse:searchresults-only></gcse:searchresults-only>
   </div>
 {% endblock %}

doc/utils/sphinx-config/false_positives.txt

@@ -1346,6 +1346,7 @@ hiID
 Hijazi
 Hilger
 Hinestrosa
+hipCUB
 hipFFT
 histo
 histogrammed

examples/COUPLE/fortran2/LAMMPS.F90

@@ -1105,7 +1105,7 @@ contains !! Wrapper functions local to this module {{{1
       C_xy = xy
       C_xz = xz
       C_yz = yz
-      call lammps_actual_reset_box (ptr, C_boxlo, C_boxhi, C_xy, C_xz, C_yz)
+      call lammps_actual_reset_box (ptr, C_boxlo, C_boxhi, C_xy, C_yz, C_xz)
    end subroutine lammps_reset_box
 
 ! lammps_gather_atoms {{{2

examples/COUPLE/fortran2/README

@@ -40,7 +40,7 @@ the dynamically-linkable library (liblammps_fortran.so).
  (2) Copy said library to your Fortran program's source directory or replace
      ${LAMMPS_LIB} with its full path in the instructions below.
  (3) Compile (but don't link!) LAMMPS.F90.  Example:
-        mpif90 -c LAMMPS.f90
+        mpifort -c LAMMPS.f90
      OR
         gfortran -c LAMMPS.F90
      NOTE:  you may get a warning such as,
@@ -72,8 +72,8 @@ the dynamically-linkable library (liblammps_fortran.so).
      were part of the usual LAMMPS library interface (if you have the module
      file visible to the compiler, that is).
  (6) Compile (but don't link) your Fortran program.  Example:
-        mpif90 -c myfreeformatfile.f90
+        mpifort -c myfreeformatfile.f90
-        mpif90 -c myfixedformatfile.f
+        mpifort -c myfixedformatfile.f
      OR
         gfortran -c myfreeformatfile.f90
         gfortran -c myfixedformatfile.f
@@ -83,12 +83,12 @@ the dynamically-linkable library (liblammps_fortran.so).
      IMPORTANT:  If the Fortran module from part (3) is not in the current
      directory or in one searched by the compiler for module files, you will
      need to include that location via the -I flag to the compiler, like so:
-        mpif90 -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
+        mpifort -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
 
  (7) Link everything together, including any libraries needed by LAMMPS (such
      as the C++ standard library, the C math library, the JPEG library, fftw,
      etc.)  For example,
-        mpif90 LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
+        mpifort LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
             ${LAMMPS_LIB} -lmpi_cxx -lstdc++ -lm
      OR
         gfortran LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
@@ -105,17 +105,17 @@ You should now have a working executable.
  (1) Compile LAMMPS as a dynamic library
      (make makeshlib && make -f Makefile.shlib [targetname]).
  (2) Compile, but don't link, LAMMPS.F90 using the -fPIC flag, such as
-        mpif90 -fPIC -c LAMMPS.f90
+        mpifort -fPIC -c LAMMPS.f90
  (3) Compile, but don't link, LAMMPS-wrapper.cpp in the same manner, e.g.
         mpicxx -fPIC -c LAMMPS-wrapper.cpp
  (4) Make the dynamic library, like so:
-        mpif90 -fPIC -shared -o liblammps_fortran.so LAMMPS.o LAMMPS-wrapper.o
+        mpifort -fPIC -shared -o liblammps_fortran.so LAMMPS.o LAMMPS-wrapper.o
  (5) Compile your program, such as,
-        mpif90 -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
+        mpifort -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
      where ${LAMMPS_SRC}/examples/COUPLE/fortran2 contains the .mod file from
      step (3)
  (6) Link everything together, such as
-        mpif90 ${my_object_files} -L${LAMMPS_SRC} \
+        mpifort ${my_object_files} -L${LAMMPS_SRC} \
             -L${LAMMPS_SRC}/examples/COUPLE/fortran2 -llammps_fortran \
             -llammps_openmpi -lmpi_cxx -lstdc++ -lm
 

examples/COUPLE/lammps_spparks/README

@@ -31,7 +31,7 @@ spkpath.h           contains path to SPPARKS home directory
 After editing the Makefile, lmppath.h, and spkpath.h to make them
 suitable for your box, type:
 
-g++ -f Makefile.g++
+make -f Makefile.g++
 
 and you should get the lmpspk executable.
 

examples/neb/in.neb.hop1

@@ -1,66 +1,66 @@
 # 2d NEB surface simulation, hop from surface to become adatom
 
-dimension	2
+dimension       2
-boundary	p s p
+boundary        p s p
 
-atom_style	atomic
+atom_style      atomic
-neighbor	0.3 bin
+neighbor        0.3 bin
-neigh_modify	delay 5
+neigh_modify    delay 5
-atom_modify	map array sort 0 0.0
+atom_modify     map array sort 0 0.0
 
-variable	u uloop 20
+variable        u uloop 20
 
 # create geometry with flat surface
 
-lattice		hex 0.9
+lattice         hex 0.9
-region		box block 0 20 0 10 -0.25 0.25
+region          box block 0 20 0 10 -0.25 0.25
 
-#create_box	3 box
+#create_box     3 box
-#create_atoms	1 box
+#create_atoms   1 box
-#mass		* 1.0
+#mass           * 1.0
 #write_data      initial.hop1
 
 read_data        initial.hop1
 
 # LJ potentials
 
-pair_style	lj/cut 2.5
+pair_style      lj/cut 2.5
-pair_coeff	* * 1.0 1.0 2.5
+pair_coeff      * * 1.0 1.0 2.5
-pair_modify	shift yes
+pair_modify     shift yes
 
 # initial minimization to relax surface
 
-minimize	1.0e-6 1.0e-4 1000 10000
+minimize        1.0e-6 1.0e-4 1000 10000
-reset_timestep	0
+reset_timestep  0
 
 # define groups
 
-region	        1 block INF INF INF 1.25 INF INF
+region          1 block INF INF INF 1.25 INF INF
-group		lower region 1
+group           lower region 1
-group		mobile subtract all lower
+group           mobile subtract all lower
-set		group lower type 2
+set             group lower type 2
 
-timestep	0.05
+timestep        0.05
 
 # group of NEB atoms - either block or single atom ID 412
 
-region		surround block 10 18 17 20 0 0 units box
+region          surround block 10 18 17 20 0 0 units box
-group		nebatoms region surround
+group           nebatoms region surround
-#group		nebatoms id 412
+#group          nebatoms id 412
-set		group nebatoms type 3
+set             group nebatoms type 3
-group		nonneb subtract all nebatoms
+group           nonneb subtract all nebatoms
 
-fix		1 lower setforce 0.0 0.0 0.0
+fix             1 lower setforce 0.0 0.0 0.0
-fix		2 nebatoms neb 1.0 parallel ideal
+fix             2 nebatoms neb 1.0 parallel ideal
-fix		3 all enforce2d
+fix             3 all enforce2d
 
-thermo		100
+thermo          100
 
-#dump		1 nebatoms atom 10 dump.neb.$u
+#dump            1 nebatoms atom 10 dump.neb.$u
-#dump		2 nonneb atom 10 dump.nonneb.$u
+#dump            2 nonneb atom 10 dump.nonneb.$u
 
 # run NEB for 2000 steps or to force tolerance
 
-min_style	quickmin
+min_style       quickmin
 
-neb		0.0 0.1 1000 1000 100 final final.hop1
+neb             0.0 0.1 1000 1000 100 final final.hop1

examples/neb/in.neb.hop1.end

@@ -1,56 +1,56 @@
 # 2d NEB surface simulation, hop from surface to become adatom
 
-dimension	2
+dimension       2
-boundary	p s p
+boundary        p s p
 
-atom_style	atomic
+atom_style      atomic
-neighbor	0.3 bin
+neighbor        0.3 bin
-neigh_modify	delay 5
+neigh_modify    delay 5
-atom_modify	map array sort 0 0.0
+atom_modify     map array sort 0 0.0
 
-variable	u uloop 20
+variable        u uloop 20
 
 # create geometry with flat surface
 
-lattice		hex 0.9
+lattice         hex 0.9
-region		box block 0 20 0 10 -0.25 0.25
+region          box block 0 20 0 10 -0.25 0.25
 
 read_data        initial.hop1.end
 
 # LJ potentials
 
-pair_style	lj/cut 2.5
+pair_style      lj/cut 2.5
-pair_coeff	* * 1.0 1.0 2.5
+pair_coeff      * * 1.0 1.0 2.5
-pair_modify	shift yes
+pair_modify     shift yes
 
 # define groups
 
-region	        1 block INF INF INF 1.25 INF INF
+region          1 block INF INF INF 1.25 INF INF
-group		lower region 1
+group           lower region 1
-group		mobile subtract all lower
+group           mobile subtract all lower
-set		group lower type 2
+set             group lower type 2
 
-timestep	0.05
+timestep        0.05
 
 # group of NEB atoms - either block or single atom ID 412
 
-region		surround block 10 18 17 20 0 0 units box
+region          surround block 10 18 17 20 0 0 units box
-group		nebatoms region surround
+group           nebatoms region surround
-#group		nebatoms id 412
+#group          nebatoms id 412
-set		group nebatoms type 3
+set             group nebatoms type 3
-group		nonneb subtract all nebatoms
+group           nonneb subtract all nebatoms
 
-fix		1 lower setforce 0.0 0.0 0.0
+fix             1 lower setforce 0.0 0.0 0.0
-fix		2 nebatoms neb 1.0 parallel ideal end first 1.0
+fix             2 nebatoms neb 1.0 parallel ideal end first 1.0
-fix		3 all enforce2d
+fix             3 all enforce2d
 
-thermo		100
+thermo          100
 
-#dump		1 nebatoms atom 10 dump.neb.$u
+#dump            1 nebatoms atom 10 dump.neb.$u
-#dump		2 nonneb atom 10 dump.nonneb.$u
+#dump            2 nonneb atom 10 dump.nonneb.$u
 
 # run NEB for 2000 steps or to force tolerance
 
-min_style	quickmin
+min_style       quickmin
 
-neb		0.0 0.1 1000 1000 100 final final.hop1
+neb             0.0 0.1 1000 1000 100 final final.hop1

examples/neb/in.neb.hop2

@@ -1,68 +1,68 @@
 # 2d NEB surface simulation, hop of adatom on surface
 
-dimension	2
+dimension       2
-boundary	p s p
+boundary        p s p
 
-atom_style	atomic
+atom_style      atomic
-neighbor	0.3 bin
+neighbor        0.3 bin
-neigh_modify	delay 5
+neigh_modify    delay 5
-atom_modify	map array sort 0 0.0
+atom_modify     map array sort 0 0.0
 
-variable	u uloop 20
+variable        u uloop 20
 
 # create geometry with adatom
 
-lattice		hex 0.9
+lattice         hex 0.9
-region		box block 0 20 0 11 -0.25 0.25
+region          box block 0 20 0 11 -0.25 0.25
-region		box1 block 0 20 0 10 -0.25 0.25
+region          box1 block 0 20 0 10 -0.25 0.25
 
-#create_box	3 box
+#create_box     3 box
-#create_atoms	1 region box1
+#create_atoms   1 region box1
-#create_atoms	1 single 11.5 10.5 0
+#create_atoms   1 single 11.5 10.5 0
-#mass		* 1.0
+#mass           * 1.0
 #write_data      initial.hop2
 
 read_data        initial.hop2
 
 # LJ potentials
 
-pair_style	lj/cut 2.5
+pair_style      lj/cut 2.5
-pair_coeff	* * 1.0 1.0 2.5
+pair_coeff      * * 1.0 1.0 2.5
-pair_modify	shift yes
+pair_modify     shift yes
 
 # initial minimization to relax surface
 
-minimize	1.0e-6 1.0e-4 1000 10000
+minimize        1.0e-6 1.0e-4 1000 10000
-reset_timestep	0
+reset_timestep  0
 
 # define groups
 
-region	        1 block INF INF INF 1.25 INF INF
+region          1 block INF INF INF 1.25 INF INF
-group		lower region 1
+group           lower region 1
-group		mobile subtract all lower
+group           mobile subtract all lower
-set		group lower type 2
+set             group lower type 2
 
-timestep	0.05
+timestep        0.05
 
 # group of NEB atoms - either block or single atom ID 421
 
-region		surround block 10 18 17 21 0 0 units box
+region          surround block 10 18 17 21 0 0 units box
-group		nebatoms region surround
+group           nebatoms region surround
-#group		nebatoms id 421
+#group          nebatoms id 421
-set		group nebatoms type 3
+set             group nebatoms type 3
-group		nonneb subtract all nebatoms
+group           nonneb subtract all nebatoms
 
-fix		1 lower setforce 0.0 0.0 0.0
+fix             1 lower setforce 0.0 0.0 0.0
-fix		2 nebatoms neb 1.0 
+fix             2 nebatoms neb 1.0
-fix		3 all enforce2d
+fix             3 all enforce2d
 
-thermo		100
+thermo          100
 
-#dump		1 nebatoms atom 10 dump.neb.$u
+#dump            1 nebatoms atom 10 dump.neb.$u
-#dump		2 nonneb atom 10 dump.nonneb.$u
+#dump            2 nonneb atom 10 dump.nonneb.$u
 
 # run NEB for 2000 steps or to force tolerance
 
-min_style	fire
+min_style       fire
 
-neb		0.0 0.05 1000 1000 100 final final.hop2
+neb             0.0 0.05 1000 1000 100 final final.hop2

examples/neb/in.neb.sivac

@@ -5,7 +5,7 @@ units           metal
 atom_style      atomic
 atom_modify     map array
 boundary        p p p
-atom_modify	sort 0 0.0
+atom_modify     sort 0 0.0
 
 # coordination number cutoff
 
@@ -45,7 +45,7 @@ group Si type 1
 group del id 300
 delete_atoms group del compress no
 group vacneigh id 174 175 301 304 306 331 337
- 
+
 # choose potential
 
 pair_style      sw
@@ -53,26 +53,26 @@ pair_coeff * * Si.sw Si
 
 # set up neb run
 
-variable	u uloop 20
+variable        u uloop 20
+
+# initial minimization to relax vacancy
+
+displace_atoms all random 0.1 0.1 0.1 123456
+minimize        1.0e-6 1.0e-4 1000 10000
+
+reset_timestep  0
 
 # only output atoms near vacancy
 
 #dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z
 
-# initial minimization to relax vacancy
+fix             1 all neb 1.0
 
-displace_atoms all random 0.1 0.1 0.1 123456
+thermo          100
-minimize	1.0e-6 1.0e-4 1000 10000
-
-reset_timestep	0
-
-fix		1 all neb 1.0 
-
-thermo		100
 
 # run NEB for 2000 steps or to force tolerance
 
 timestep        0.01
-min_style	quickmin
+min_style       quickmin
 
-neb		0.0 0.01 100 100 10 final final.sivac
+neb             0.0 0.01 100 100 10 final final.sivac

fortran/lammps.f90

@@ -54,20 +54,18 @@ MODULE LIBLAMMPS
 
   ! interface definitions for calling functions in library.cpp
   INTERFACE
-      FUNCTION lammps_open(argc,argv,comm) &
+      FUNCTION lammps_open(argc, argv, comm) BIND(C, name='lammps_open_fortran')
-          BIND(C, name='lammps_open_fortran')
         IMPORT :: c_ptr, c_int
         INTEGER(c_int), VALUE, INTENT(in)     :: argc, comm
         TYPE(c_ptr), DIMENSION(*), INTENT(in) :: argv
         TYPE(c_ptr)                           :: lammps_open
       END FUNCTION lammps_open
 
-      FUNCTION lammps_open_no_mpi(argc,argv,handle) &
+      FUNCTION lammps_open_no_mpi(argc, argv, handle) BIND(C, name='lammps_open_no_mpi')
-          BIND(C, name='lammps_open_no_mpi')
         IMPORT :: c_ptr, c_int
         INTEGER(c_int), VALUE, INTENT(in)     :: argc
         TYPE(c_ptr), DIMENSION(*), INTENT(in) :: argv
-        TYPE(c_ptr), INTENT(out)              :: handle
+        TYPE(c_ptr), VALUE, INTENT(in)        :: handle
         TYPE(c_ptr)                           :: lammps_open_no_mpi
       END FUNCTION lammps_open_no_mpi
 
@@ -85,28 +83,26 @@ MODULE LIBLAMMPS
       SUBROUTINE lammps_kokkos_finalize() BIND(C, name='lammps_kokkos_finalize')
       END SUBROUTINE lammps_kokkos_finalize
 
-      SUBROUTINE lammps_file(handle,filename) BIND(C, name='lammps_file')
+      SUBROUTINE lammps_file(handle, filename) BIND(C, name='lammps_file')
         IMPORT :: c_ptr
         TYPE(c_ptr), VALUE :: handle
         TYPE(c_ptr), VALUE :: filename
       END SUBROUTINE lammps_file
 
-      SUBROUTINE lammps_command(handle,cmd) BIND(C, name='lammps_command')
+      SUBROUTINE lammps_command(handle, cmd) BIND(C, name='lammps_command')
         IMPORT :: c_ptr
         TYPE(c_ptr), VALUE :: handle
         TYPE(c_ptr), VALUE :: cmd
       END SUBROUTINE lammps_command
 
-      SUBROUTINE lammps_commands_list(handle,ncmd,cmds) &
+      SUBROUTINE lammps_commands_list(handle, ncmd, cmds) BIND(C, name='lammps_commands_list')
-          BIND(C, name='lammps_commands_list')
         IMPORT :: c_ptr, c_int
         TYPE(c_ptr), VALUE :: handle
         INTEGER(c_int), VALUE, INTENT(in)     :: ncmd
         TYPE(c_ptr), DIMENSION(*), INTENT(in) :: cmds
       END SUBROUTINE lammps_commands_list
 
-      SUBROUTINE lammps_commands_string(handle,str) &
+      SUBROUTINE lammps_commands_string(handle, str) BIND(C, name='lammps_commands_string')
-          BIND(C, name='lammps_commands_string')
         IMPORT :: c_ptr
         TYPE(c_ptr), VALUE :: handle
         TYPE(c_ptr), VALUE :: str
@@ -137,24 +133,22 @@ MODULE LIBLAMMPS
   END INTERFACE
 
 CONTAINS
-
   ! Fortran wrappers and helper functions.
 
   ! Constructor for the LAMMPS class.
   ! Combined wrapper around lammps_open_fortran() and lammps_open_no_mpi()
-  TYPE(lammps) FUNCTION lmp_open(args,comm)
+  TYPE(lammps) FUNCTION lmp_open(args, comm)
     IMPLICIT NONE
-    INTEGER,INTENT(in), OPTIONAL :: comm
+    INTEGER, INTENT(in), OPTIONAL :: comm
     CHARACTER(len=*), INTENT(in), OPTIONAL :: args(:)
     TYPE(c_ptr), ALLOCATABLE     :: argv(:)
-    TYPE(c_ptr)                  :: dummy=c_null_ptr
+    INTEGER(c_int)               :: i, c_comm, argc
-    INTEGER :: i,argc
 
     IF (PRESENT(args)) THEN
-        ! convert argument list to c style
+        ! convert fortran argument list to c style
         argc = SIZE(args)
         ALLOCATE(argv(argc))
-        DO i=1,argc
+        DO i=1, argc
            argv(i) = f2c_string(args(i))
         END DO
     ELSE
@@ -164,23 +158,24 @@ CONTAINS
     ENDIF
 
     IF (PRESENT(comm)) THEN
-        lmp_open%handle = lammps_open(argc,argv,comm)
+        c_comm = comm
+        lmp_open%handle = lammps_open(argc, argv, c_comm)
     ELSE
-        lmp_open%handle = lammps_open_no_mpi(argc,argv,dummy)
+        lmp_open%handle = lammps_open_no_mpi(argc, argv, c_null_ptr)
     END IF
 
     ! Clean up allocated memory
-    DO i=1,argc
+    DO i=1, argc
         CALL lammps_free(argv(i))
     END DO
     DEALLOCATE(argv)
   END FUNCTION lmp_open
 
   ! Combined Fortran wrapper around lammps_close() and lammps_mpi_finalize()
-  SUBROUTINE lmp_close(self,finalize)
+  SUBROUTINE lmp_close(self, finalize)
     IMPLICIT NONE
     CLASS(lammps) :: self
-    LOGICAL,INTENT(in),OPTIONAL :: finalize
+    LOGICAL, INTENT(in), OPTIONAL :: finalize
 
     CALL lammps_close(self%handle)
 
@@ -206,68 +201,69 @@ CONTAINS
     lmp_get_natoms = lammps_get_natoms(self%handle)
   END FUNCTION lmp_get_natoms
 
-  SUBROUTINE lmp_file(self,filename)
+  SUBROUTINE lmp_file(self, filename)
     IMPLICIT NONE
     CLASS(lammps) :: self
     CHARACTER(len=*) :: filename
     TYPE(c_ptr) :: str
 
     str = f2c_string(filename)
-    CALL lammps_file(self%handle,str)
+    CALL lammps_file(self%handle, str)
     CALL lammps_free(str)
   END SUBROUTINE lmp_file
 
   ! equivalent function to lammps_command()
-  SUBROUTINE lmp_command(self,cmd)
+  SUBROUTINE lmp_command(self, cmd)
     IMPLICIT NONE
     CLASS(lammps) :: self
     CHARACTER(len=*) :: cmd
     TYPE(c_ptr) :: str
 
     str = f2c_string(cmd)
-    CALL lammps_command(self%handle,str)
+    CALL lammps_command(self%handle, str)
     CALL lammps_free(str)
   END SUBROUTINE lmp_command
 
   ! equivalent function to lammps_commands_list()
-  SUBROUTINE lmp_commands_list(self,cmds)
+  SUBROUTINE lmp_commands_list(self, cmds)
     IMPLICIT NONE
     CLASS(lammps) :: self
     CHARACTER(len=*), INTENT(in), OPTIONAL :: cmds(:)
     TYPE(c_ptr), ALLOCATABLE     :: cmdv(:)
-    INTEGER :: i,ncmd
+    INTEGER :: i, ncmd
 
     ! convert command list to c style
     ncmd = SIZE(cmds)
     ALLOCATE(cmdv(ncmd))
-    DO i=1,ncmd
+    DO i=1, ncmd
         cmdv(i) = f2c_string(cmds(i))
     END DO
 
-    CALL lammps_commands_list(self%handle,ncmd,cmdv)
+    CALL lammps_commands_list(self%handle, ncmd, cmdv)
 
     ! Clean up allocated memory
-    DO i=1,ncmd
+    DO i=1, ncmd
         CALL lammps_free(cmdv(i))
     END DO
     DEALLOCATE(cmdv)
   END SUBROUTINE lmp_commands_list
 
   ! equivalent function to lammps_commands_string()
-  SUBROUTINE lmp_commands_string(self,str)
+  SUBROUTINE lmp_commands_string(self, str)
     IMPLICIT NONE
     CLASS(lammps) :: self
     CHARACTER(len=*) :: str
     TYPE(c_ptr) :: tmp
 
     tmp = f2c_string(str)
-    CALL lammps_commands_string(self%handle,tmp)
+    CALL lammps_commands_string(self%handle, tmp)
     CALL lammps_free(tmp)
   END SUBROUTINE lmp_commands_string
 
   ! ----------------------------------------------------------------------
   ! local helper functions
   ! copy fortran string to zero terminated c string
+  ! ----------------------------------------------------------------------
   FUNCTION f2c_string(f_string) RESULT(ptr)
     CHARACTER (len=*), INTENT(in)           :: f_string
     CHARACTER (len=1, kind=c_char), POINTER :: c_string(:)
@@ -276,8 +272,8 @@ CONTAINS
 
     n = LEN_TRIM(f_string)
     ptr = lammps_malloc(n+1)
-    CALL C_F_POINTER(ptr,c_string,[1])
+    CALL C_F_POINTER(ptr, c_string, [1])
-    DO i=1,n
+    DO i=1, n
         c_string(i) = f_string(i:i)
     END DO
     c_string(n+1) = c_null_char

lib/atc/ExtrinsicModelElectrostatic.cpp

@@ -787,8 +787,7 @@ namespace ATC {
       xtArgs[3] = 1.; xtArgs[4] = 1.; xtArgs[5] = 1.;
       xtArgs[6] = coulombConstant*chargeDensity;
       xtArgs[7] = -1.;
-      string radialPower = "radial_power";
+      f = XT_Function_Mgr::instance()->function("radial_power",8,xtArgs);
-      f = XT_Function_Mgr::instance()->function(radialPower,8,xtArgs);
 
 
       for (iset = faceset->begin(); iset != faceset->end(); iset++) {

lib/atc/FE_Element.cpp

@@ -186,7 +186,7 @@ static const double localCoordinatesTolerance = 1.e-09;
       double c[3]={0,0,0};
       c[0] = y0*X[0] - y0*X[1] - y0*X[2] + y0*X[3] - x0*Y[0] + (X[1]*Y[0])*0.5 + (X[2]*Y[0])*0.5 + x0*Y[1] - (X[0]*Y[1])*0.5 - (X[3]*Y[1])*0.5 + x0*Y[2] - (X[0]*Y[2])*0.5 - (X[3]*Y[2])*0.5 - x0*Y[3] + (X[1]*Y[3])*0.5 + (X[2]*Y[3])*0.5;
       c[1] = -(y0*X[0]) + y0*X[1] - y0*X[2] + y0*X[3] + x0*Y[0] - X[1]*Y[0] - x0*Y[1] + X[0]*Y[1] + x0*Y[2] - X[3]*Y[2] - x0*Y[3] + X[2]*Y[3];
-      c[1] = (X[1]*Y[0])*0.5 - (X[2]*Y[0])*0.5 - (X[0]*Y[1])*0.5 + (X[3]*Y[1])*0.5 + (X[0]*Y[2])*0.5 - (X[3]*Y[2])*0.5 - (X[1]*Y[3])*0.5 + (X[2]*Y[3])*0.5;
+      c[2] = (X[1]*Y[0])*0.5 - (X[2]*Y[0])*0.5 - (X[0]*Y[1])*0.5 + (X[3]*Y[1])*0.5 + (X[0]*Y[2])*0.5 - (X[3]*Y[2])*0.5 - (X[1]*Y[3])*0.5 + (X[2]*Y[3])*0.5;
       double xi2[2]={0,0};
       int nroots = solve_quadratic(c,xi2);
       if (nroots == 0) throw ATC_Error("no real roots in 2D analytic projection guess");

lib/atc/Function.cpp

@@ -48,7 +48,7 @@ namespace ATC {
   }
 
   // add user function into the if statement and assign returnFunction to it
-  UXT_Function* UXT_Function_Mgr::function(string & type, int nargs, double * args)
+  UXT_Function* UXT_Function_Mgr::function(const string & type, int nargs, double * args)
   {
     UXT_Function * returnFunction;
     if      (type=="linear") {
@@ -167,7 +167,7 @@ XT_Function_Mgr * XT_Function_Mgr::myInstance_ = nullptr;
   }
 
   // add user function into the if statement and assign returnFunction to it
-  XT_Function* XT_Function_Mgr::function(string & type, int nargs, double * args)
+  XT_Function* XT_Function_Mgr::function(const string & type, int nargs, double * args)
   {
     XT_Function * returnFunction;
     if      (type=="constant") {

lib/atc/Function.h

@@ -110,7 +110,7 @@ namespace ATC {
     /** Static instance of this class */
     static UXT_Function_Mgr * instance();
 
-    UXT_Function* function(std::string & type, int nargs, double * arg);
+    UXT_Function* function(const std::string & type, int nargs, double * arg);
     UXT_Function* function(char ** arg, int nargs);
     UXT_Function* linear_function(double c0, double c1);
     UXT_Function* copy_UXT_function(UXT_Function* other);
@@ -181,7 +181,7 @@ namespace ATC {
     /** Static instance of this class */
     static XT_Function_Mgr * instance();
 
-    XT_Function* function(std::string & type, int nargs, double * arg);
+    XT_Function* function(const std::string & type, int nargs, double * arg);
     XT_Function* function(char ** arg, int nargs);
     XT_Function* constant_function(double c);
     XT_Function* copy_XT_function(XT_Function* other);

python/examples/pizza/dump.py

@@ -1,4 +1,4 @@
-# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
+# Pizza.py toolkit, https://lammps.github.io/pizza
 # Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
 #
 # Copyright (2005) Sandia Corporation.  Under the terms of Contract

python/examples/pizza/gl.py

@@ -1,4 +1,4 @@
-# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
+# Pizza.py toolkit, https://lammps.github.io/pizza
 # Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
 #
 # Copyright (2005) Sandia Corporation.  Under the terms of Contract

python/examples/pizza/gnu.py

@@ -1,4 +1,4 @@
-# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
+# Pizza.py toolkit, https://lammps.github.io/pizza
 # Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
 #
 # Copyright (2005) Sandia Corporation.  Under the terms of Contract

python/examples/pizza/pdbfile.py

@@ -1,4 +1,4 @@
-# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
+# Pizza.py toolkit, https://lammps.github.io/pizza
 # Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
 #
 # Copyright (2005) Sandia Corporation.  Under the terms of Contract

python/examples/pizza/vizinfo.py

@@ -1,4 +1,4 @@
-# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
+# Pizza.py toolkit, https://lammps.github.io/pizza
 # Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
 #
 # Copyright (2005) Sandia Corporation.  Under the terms of Contract

python/examples/pizza/vmd.py

@@ -1,4 +1,4 @@
-# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
+# Pizza.py toolkit, https://lammps.github.io/pizza
 # Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
 #
 # Copyright (2005) Sandia Corporation.  Under the terms of Contract

python/lammps/mliap/__init__.py

@@ -4,17 +4,29 @@
 # try to improperly start up a new interpreter.
 import sysconfig
 import ctypes
-library = sysconfig.get_config_vars('INSTSONAME')[0]
+import platform
+
+py_ver = sysconfig.get_config_vars('VERSION')[0]
+OS_name = platform.system()
+
+if OS_name == "Linux":
+    SHLIB_SUFFIX = '.so'
+    library = 'libpython' + py_ver + SHLIB_SUFFIX
+elif OS_name == "Darwin":
+    SHLIB_SUFFIX = '.dylib'
+    library = 'libpython' + py_ver + SHLIB_SUFFIX
+elif OS_name == "Windows":
+    SHLIB_SUFFIX = '.dll'
+    library = 'python' + py_ver + SHLIB_SUFFIX
+
 try:
     pylib = ctypes.CDLL(library)
-except OSError as e:
+except Exception as e:
-    if pylib.endswith(".a"):
+    raise OSError("Unable to locate python shared library") from e
-        pylib.strip(".a") + ".so"
+
-        pylib = ctypes.CDLL(library)
-    else:
-        raise e
 if not pylib.Py_IsInitialized():
     raise RuntimeError("This interpreter is not compatible with python-based mliap for LAMMPS.")
+
 del sysconfig, ctypes, library, pylib
 
 from .loader import load_model, load_unified, activate_mliappy

src/AMOEBA/amoeba_hal.cpp

@@ -16,12 +16,17 @@
 
 #include "atom.h"
 #include "error.h"
+#include "math_special.h"
 #include "neigh_list.h"
 
 #include <cmath>
 
 using namespace LAMMPS_NS;
 
+using MathSpecial::square;
+using MathSpecial::cube;
+using MathSpecial::powint;
+
 enum{VDWL,REPULSE,QFER,DISP,MPOLE,POLAR,USOLV,DISP_LONG,MPOLE_LONG,POLAR_LONG};
 
 /* ----------------------------------------------------------------------
@@ -114,14 +119,14 @@ void PairAmoeba::hal()
       }
       eps *= factor_hal;
 
-      rv7 = pow(rv,7.0);
+      rv7 = powint(rv,7);
-      rik6 = pow(rik2,3.0);
+      rik6 = cube(rik2);
       rik7 = rik6 * rik;
       rho = rik7 + ghal*rv7;
       tau = (dhal+1.0) / (rik + dhal*rv);
-      tau7 = pow(tau,7.0);
+      tau7 = powint(tau,7);
       dtau = tau / (dhal+1.0);
-      gtau = eps*tau7*rik6*(ghal+1.0)*pow(rv7/rho,2.0);
+      gtau = eps*tau7*rik6*(ghal+1.0)*square(rv7/rho);
       e = eps*tau7*rv7*((ghal+1.0)*rv7/rho-2.0);
       de = -7.0 * (dtau*e+gtau);
 

src/AMOEBA/amoeba_induce.cpp

@@ -20,8 +20,9 @@
 #include "domain.h"
 #include "error.h"
 #include "fft3d_wrap.h"
-#include "fix_store.h"
+#include "fix_store_peratom.h"
 #include "math_const.h"
+#include "math_special.h"
 #include "memory.h"
 #include "my_page.h"
 #include "neigh_list.h"
@@ -32,6 +33,8 @@
 using namespace LAMMPS_NS;
 using namespace MathConst;
 
+using MathSpecial::cube;
+
 enum{INDUCE,RSD,SETUP_AMOEBA,SETUP_HIPPO,KMPOLE,AMGROUP};   // forward comm
 enum{FIELD,ZRSD,TORQUE,UFLD};                               // reverse comm
 enum{VDWL,REPULSE,QFER,DISP,MPOLE,POLAR,USOLV,DISP_LONG,MPOLE_LONG,POLAR_LONG};
@@ -366,7 +369,8 @@ void PairAmoeba::induce()
       eps = DEBYE * sqrt(eps/atom->natoms);
 
       if (eps < poleps) done = true;
-      if (eps > epsold) done = true;
+      // also commented out in induce.f of Tinker
+      // if (eps > epsold) done = true;
       if (iter >= politer) done = true;
 
       //  apply a "peek" iteration to the mutual induced dipoles
@@ -387,7 +391,7 @@ void PairAmoeba::induce()
     // terminate the calculation if dipoles failed to converge
     // NOTE: could make this an error
 
-    if (iter >= maxiter || eps > epsold)
+    if (iter >= politer || eps > epsold)
       if (comm->me == 0)
         error->warning(FLERR,"AMOEBA induced dipoles did not converge");
   }
@@ -732,7 +736,7 @@ void PairAmoeba::uscale0b(int mode, double **rsd, double **rsdp,
         damp = pdi * pdamp[jtype];
         if (damp != 0.0) {
           pgamma = MIN(pti,thole[jtype]);
-          damp = -pgamma * pow((r/damp),3.0);
+          damp = -pgamma * cube(r/damp);
           if (damp > -50.0) {
             expdamp = exp(damp);
             scale3 *= 1.0 - expdamp;
@@ -1332,7 +1336,7 @@ void PairAmoeba::udirect2b(double **field, double **fieldp)
             }
           } else {
             pgamma = MIN(pti,thole[jtype]);
-            damp = pgamma * pow(r/damp,3.0);
+            damp = pgamma * cube(r/damp);
             if (damp < 50.0) {
               expdamp = exp(-damp);
               scale3 = 1.0 - expdamp;
@@ -1384,7 +1388,7 @@ void PairAmoeba::udirect2b(double **field, double **fieldp)
           damp = pdi * pdamp[jtype];
           if (damp != 0.0) {
             pgamma = MIN(pti,thole[jtype]);
-            damp = pgamma * pow(r/damp,3.0);
+            damp = pgamma * cube(r/damp);
             if (damp < 50.0) {
               expdamp = exp(-damp);
               scale3 = 1.0 - expdamp;

src/AMOEBA/amoeba_kspace.cpp

@@ -17,6 +17,7 @@
 #include "atom.h"
 #include "domain.h"
 #include "math_const.h"
+#include "math_special.h"
 #include "memory.h"
 
 #include <cmath>
@@ -24,6 +25,8 @@
 using namespace LAMMPS_NS;
 using namespace MathConst;
 
+using MathSpecial::powint;
+
 #define ANINT(x) ((x)>0 ? floor((x)+0.5) : ceil((x)-0.5))
 
 /* ----------------------------------------------------------------------
@@ -173,13 +176,13 @@ void PairAmoeba::dftmod(double *bsmod, double *bsarray, int nfft, int order)
       factor = MY_PI * k / nfft;
       for (j = 1; j <= jcut; j++) {
         arg = factor / (factor + MY_PI*j);
-        sum1 += pow(arg,order);
+        sum1 += powint(arg,order);
-        sum2 += pow(arg,order2);
+        sum2 += powint(arg,order2);
       }
       for (j = 1; j <= jcut; j++) {
         arg = factor / (factor - MY_PI*j);
-        sum1 += pow(arg,order);
+        sum1 += powint(arg,order);
-        sum2 += pow(arg,order2);
+        sum2 += powint(arg,order2);
       }
       zeta = sum2 / sum1;
     }
@@ -1137,7 +1140,7 @@ void PairAmoeba::kewald()
     // NOTE: also worry about satisfying Tinker minfft ?
 
     while (!factorable(ndfft1)) ndfft1++;
-    while (!factorable(ndfft2)) ndfft3++;
+    while (!factorable(ndfft2)) ndfft2++;
     while (!factorable(ndfft3)) ndfft3++;
   }
 

src/AMOEBA/amoeba_multipole.cpp

@@ -20,6 +20,7 @@
 #include "domain.h"
 #include "fft3d_wrap.h"
 #include "math_const.h"
+#include "math_special.h"
 #include "memory.h"
 #include "neigh_list.h"
 
@@ -29,6 +30,8 @@
 using namespace LAMMPS_NS;
 using namespace MathConst;
 
+using MathSpecial::square;
+
 enum{FIELD,ZRSD,TORQUE,UFLD};                          // reverse comm
 enum{VDWL,REPULSE,QFER,DISP,MPOLE,POLAR,USOLV,DISP_LONG,MPOLE_LONG,POLAR_LONG};
 
@@ -670,7 +673,7 @@ void PairAmoeba::multipole_kspace()
   nzlo = m_kspace->nzlo_fft;
   nzhi = m_kspace->nzhi_fft;
 
-  pterm = pow((MY_PI/aewald),2.0);
+  pterm = square(MY_PI/aewald);
   volterm = MY_PI * volbox;
 
   n = 0;

src/AMOEBA/amoeba_polar.cpp

@@ -20,6 +20,7 @@
 #include "domain.h"
 #include "fft3d_wrap.h"
 #include "math_const.h"
+#include "math_special.h"
 #include "memory.h"
 #include "neigh_list.h"
 
@@ -29,6 +30,9 @@
 using namespace LAMMPS_NS;
 using namespace MathConst;
 
+using MathSpecial::square;
+using MathSpecial::cube;
+
 enum{FIELD,ZRSD,TORQUE,UFLD};                          // reverse comm
 enum{MUTUAL,OPT,TCG,DIRECT};
 enum{VDWL,REPULSE,QFER,DISP,MPOLE,POLAR,USOLV,DISP_LONG,MPOLE_LONG,POLAR_LONG};
@@ -82,7 +86,7 @@ void PairAmoeba::polar()
 
   // compute the Ewald self-energy torque and virial terms
 
-  term = (4.0/3.0) * felec * pow(aewald,3.0) / MY_PIS;
+  term = (4.0/3.0) * felec * cube(aewald) / MY_PIS;
 
   for (i = 0; i < nlocal; i++) {
     dix = rpole[i][1];
@@ -454,7 +458,7 @@ void PairAmoeba::polar_real()
         damp = pdi * pdamp[jtype];
         if (damp != 0.0) {
           pgamma = MIN(pti,thole[jtype]);
-          damp = pgamma * pow(r/damp,3.0);
+          damp = pgamma * cube(r/damp);
           if (damp < 50.0) {
             expdamp = exp(-damp);
             sc3 = 1.0 - expdamp;
@@ -499,6 +503,18 @@ void PairAmoeba::polar_real()
             urc3[k] = rc3[k] * factor_uscale;
             urc5[k] = rc5[k] * factor_uscale;
           }
+        } else {
+          // avoid uninitialized data access when damp == 0.0
+          psc3 = psc5 = psc7 = dsc3 = dsc5 = dsc7 = usc3 = usc5 = 0.0;
+          psr3 = psr5 = psr7 = dsr3 = dsr5 = dsr7 = usr5 = 0.0;
+          prc3[0] = prc3[1] = prc3[2] = 0.0;
+          drc3[0] = drc3[1] = drc3[2] = 0.0;
+          prc5[0] = prc5[1] = prc5[2] = 0.0;
+          drc5[0] = drc5[1] = drc5[2] = 0.0;
+          prc7[0] = prc7[1] = prc7[2] = 0.0;
+          drc7[0] = drc7[1] = drc7[2] = 0.0;
+          urc3[0] = urc3[1] = urc3[2] = 0.0;
+          urc5[0] = urc5[1] = urc5[2] = 0.0;
         }
 
       // apply charge penetration damping to scale factors
@@ -1260,7 +1276,7 @@ void PairAmoeba::polar_kspace()
   int nlocal = atom->nlocal;
 
   double volbox = domain->prd[0] * domain->prd[1] * domain->prd[2];
-  pterm = pow((MY_PI/aewald),2.0);
+  pterm = square(MY_PI/aewald);
   volterm = MY_PI * volbox;
 
   // initialize variables required for the scalar summation

src/AMOEBA/amoeba_repulsion.cpp

@@ -504,7 +504,7 @@ void PairAmoeba::damprep(double r, double r2, double rr1, double rr3,
     dmpk24 = dmpk23 * dmpk2;
     dmpk25 = dmpk24 * dmpk2;
     term = dmpi22 - dmpk22;
-    pre = 8192.0 * dmpi23 * dmpk23 / pow(term,4.0);
+    pre = 8192.0 * dmpi23 * dmpk23 / (term*term*term*term);
     tmp = 4.0 * dmpi2 * dmpk2 / term;
     s = (dampi-tmp)*expk + (dampk+tmp)*expi;
 

src/AMOEBA/amoeba_utils.cpp

@@ -18,7 +18,7 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_store.h"
+#include "fix_store_peratom.h"
 #include "neigh_list.h"
 
 #include <cmath>
@@ -84,9 +84,9 @@ void PairAmoeba::kmpole()
         if (bondneigh[j] < smallest) {
           smallest = bondneigh[j];
           k = j;
+          bondneigh[k] = bondneigh[m];
+          bondneigh[m] = smallest;
         }
-        bondneigh[k] = bondneigh[m];
-        bondneigh[m] = smallest;
       }
     }
 
@@ -256,7 +256,7 @@ void PairAmoeba::kmpole()
       ztype = zpole[itype][iframe];
       if (ztype == 0 && !flag) {
         flag = 1;
-        xyzaxis[i][2] = xyzaxis[i][0] = xyzaxis[i][2] = 0.0;
+        xyzaxis[i][2] = xyzaxis[i][1] = xyzaxis[i][0] = 0.0;
         polaxe[i] = mpaxis[itype][iframe];
         for (j = 0; j < 13; j++)
           pole[i][j] = fpole[itype][iframe][j];

src/AMOEBA/angle_amoeba.cpp

@@ -53,6 +53,9 @@ AngleAmoeba::AngleAmoeba(LAMMPS *lmp) : Angle(lmp)
 
   ub_k = nullptr;
   ub_r0 = nullptr;
+
+  setflag_a = setflag_ba = setflag_ub = nullptr;
+  enable_angle = enable_urey = 0;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -264,6 +267,7 @@ void AngleAmoeba::tinker_anglep(int i1, int i2, int i3, int type, int eflag)
   }
 
   i4 = atom->map(i4tag);
+  if (i4 < 0) error->one(FLERR,"Amoeba angle 4th atom {} out of range", i4tag);
   i4 = domain->closest_image(i2,i4);
 
   // anglep out-of-plane calculation from Tinker

src/AMOEBA/pair_amoeba.cpp

@@ -21,10 +21,11 @@
 #include "error.h"
 #include "fft3d_wrap.h"
 #include "fix.h"
-#include "fix_store.h"
+#include "fix_store_peratom.h"
 #include "force.h"
 #include "gridcomm.h"
 #include "group.h"
+#include "math_special.h"
 #include "memory.h"
 #include "modify.h"
 #include "my_page.h"
@@ -40,6 +41,8 @@
 
 using namespace LAMMPS_NS;
 
+using MathSpecial::powint;
+
 enum{INDUCE,RSD,SETUP_AMOEBA,SETUP_HIPPO,KMPOLE,AMGROUP,PVAL};  // forward comm
 enum{FIELD,ZRSD,TORQUE,UFLD};                                   // reverse comm
 enum{ARITHMETIC,GEOMETRIC,CUBIC_MEAN,R_MIN,SIGMA,DIAMETER,HARMONIC,HHG,W_H};
@@ -780,8 +783,8 @@ void PairAmoeba::init_style()
   Fix *myfix;
   if (first_flag) {
     id_pole = utils::strdup("AMOEBA_pole");
-    myfix = modify->add_fix(fmt::format("{} {} STORE peratom 1 13",id_pole,group->names[0]));
+    myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 13",id_pole,group->names[0]));
-    fixpole = dynamic_cast<FixStore *>(myfix);
+    fixpole = dynamic_cast<FixStorePeratom *>(myfix);
   }
 
   // creation of per-atom storage
@@ -792,14 +795,14 @@ void PairAmoeba::init_style()
 
   if (first_flag && use_pred) {
     id_udalt = utils::strdup("AMOEBA_udalt");
-    myfix = modify->add_fix(fmt::format("{} {} STORE peratom 1 {} 3",
+    myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 {} 3",
                                         id_udalt, group->names[0], maxualt));
-    fixudalt = dynamic_cast<FixStore *>(myfix);
+    fixudalt = dynamic_cast<FixStorePeratom *>(myfix);
 
     id_upalt = utils::strdup("AMOEBA_upalt");
-    myfix = modify->add_fix(fmt::format("{} {} STORE peratom 1 {} 3",
+    myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 {} 3",
                                         id_upalt, group->names[0], maxualt));
-    fixupalt = dynamic_cast<FixStore *>(myfix);
+    fixupalt = dynamic_cast<FixStorePeratom *>(myfix);
   }
 
   // create pages for storing pairwise data:
@@ -913,19 +916,22 @@ void PairAmoeba::init_style()
 
   if (id_pole) {
     myfix = modify->get_fix_by_id(id_pole);
-    if (!myfix) error->all(FLERR,"Could not find internal pair amoeba fix STORE id {}", id_pole);
+    if (!myfix)
-    fixpole = dynamic_cast<FixStore *>(myfix);
+      error->all(FLERR,"Could not find internal pair amoeba fix STORE/PERATOM id {}", id_pole);
+    fixpole = dynamic_cast<FixStorePeratom *>(myfix);
 
   }
 
   if (id_udalt) {
     myfix = modify->get_fix_by_id(id_udalt);
-    if (!myfix) error->all(FLERR,"Could not find internal pair amoeba fix STORE id {}", id_udalt);
+    if (!myfix)
-    fixudalt = dynamic_cast<FixStore *>(myfix);
+      error->all(FLERR,"Could not find internal pair amoeba fix STORE/PERATOM id {}", id_udalt);
+    fixudalt = dynamic_cast<FixStorePeratom *>(myfix);
 
     myfix = modify->get_fix_by_id(id_upalt);
-    if (!myfix) error->all(FLERR,"Could not find internal pair amoeba fix STORE id {}", id_upalt);
+    if (!myfix)
-    fixupalt = dynamic_cast<FixStore *>(myfix);
+      error->all(FLERR,"Could not find internal pair amoeba fix STORE/PERATOM id {}", id_upalt);
+    fixupalt = dynamic_cast<FixStorePeratom *>(myfix);
   }
 
   // assign hydrogen neighbors (redID) to each owned atom
@@ -1956,7 +1962,7 @@ void PairAmoeba::choose(int which)
 
   // taper coeffs
 
-  double denom = pow(off-cut,5.0);
+  double denom = powint(off-cut,5);
   c0 = off*off2 * (off2 - 5.0*off*cut + 10.0*cut2) / denom;
   c1 = -30.0 * off2*cut2 / denom;
   c2 = 30.0 * (off2*cut+off*cut2) / denom;
@@ -2026,7 +2032,7 @@ void PairAmoeba::mix()
       } else if (epsilon_rule == HHG) {
         eij = 4.0 * (ei*ej) / ((sei+sej)*(sei+sej));
       } else if (epsilon_rule == W_H) {
-        eij = 2.0 * (sei*sej) * pow(ri*rj,3.0) / (pow(ri,6.0) + pow(rj,6.0));
+        eij = 2.0 * (sei*sej) * powint(ri*rj,3) / (powint(ri,6) + powint(rj,6));
       } else {
         eij = sei * sej;
       }

src/AMOEBA/pair_amoeba.h

@@ -157,9 +157,9 @@ class PairAmoeba : public Pair {
   int *amgroup;    // AMOEBA polarization group, 1 to Ngroup
 
   char *id_pole, *id_udalt, *id_upalt;
-  class FixStore *fixpole;     // stores pole = multipole components
+  class FixStorePeratom *fixpole;     // stores pole = multipole components
-  class FixStore *fixudalt;    // stores udalt = induced dipole history
+  class FixStorePeratom *fixudalt;    // stores udalt = induced dipole history
-  class FixStore *fixupalt;    // stores upalt = induced dipole history
+  class FixStorePeratom *fixupalt;    // stores upalt = induced dipole history
 
   // static per-type properties defined in force-field file
 

src/BPM/bond_bpm.cpp

@@ -84,9 +84,9 @@ void BondBPM::init_style()
 {
   if (id_fix_store_local) {
     auto ifix = modify->get_fix_by_id(id_fix_store_local);
-    if (!ifix) error->all(FLERR, "Cannot find fix store/local");
+    if (!ifix) error->all(FLERR, "Cannot find fix STORE/LOCAL id {}",id_fix_store_local);
-    if (strcmp(ifix->style, "STORE_LOCAL") != 0)
+    if (strcmp(ifix->style, "STORE/LOCAL") != 0)
-      error->all(FLERR, "Incorrect fix style matched, not store/local");
+      error->all(FLERR, "Incorrect fix style matched, not STORE/LOCAL: {}",ifix->style);
     fix_store_local = dynamic_cast<FixStoreLocal *>(ifix);
     fix_store_local->nvalues = nvalues;
   }
@@ -141,7 +141,7 @@ void BondBPM::init_style()
    global settings
    All args before store/local command are saved for potential args
      for specific bond BPM substyles
-   All args after optional store/local command are variables stored
+   All args after optional stode/local command are variables stored
      in the compute store/local
 ------------------------------------------------------------------------- */
 
@@ -202,7 +202,7 @@ void BondBPM::settings(int narg, char **arg)
     auto ifix = modify->get_fix_by_id(id_fix_store_local);
     if (!ifix)
       ifix = modify->add_fix(
-          fmt::format("{} all STORE_LOCAL {} {}", id_fix_store_local, store_local_freq, nvalues));
+          fmt::format("{} all STORE/LOCAL {} {}", id_fix_store_local, store_local_freq, nvalues));
     fix_store_local = dynamic_cast<FixStoreLocal *>(ifix);
 
     // Use property/atom to save reference positions as it can transfer to ghost atoms

src/CG-SPICA/angle_spica.cpp

@@ -21,17 +21,17 @@
 
 #include "angle_spica.h"
 
-#include <cmath>
 #include "atom.h"
-#include "neighbor.h"
-#include "pair.h"
-#include "domain.h"
 #include "comm.h"
+#include "domain.h"
+#include "error.h"
 #include "force.h"
 #include "math_const.h"
 #include "memory.h"
-#include "error.h"
+#include "neighbor.h"
+#include "pair.h"
 
+#include <cmath>
 
 #include "lj_spica_common.h"
 
@@ -43,7 +43,12 @@ using namespace LJSPICAParms;
 
 /* ---------------------------------------------------------------------- */
 
-AngleSPICA::AngleSPICA(LAMMPS *lmp) : Angle(lmp) { repflag = 0;}
+AngleSPICA::AngleSPICA(LAMMPS *lmp) :
+    Angle(lmp), k(nullptr), theta0(nullptr), lj_type(nullptr), lj1(nullptr), lj2(nullptr),
+    lj3(nullptr), lj4(nullptr), rminsq(nullptr), emin(nullptr)
+{
+  repflag = 0;
+}
 
 /* ---------------------------------------------------------------------- */
 

src/CG-SPICA/pair_lj_spica.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -19,15 +18,15 @@
 
 #include "pair_lj_spica.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "force.h"
-#include "neigh_list.h"
-#include "memory.h"
 #include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_list.h"
 
+#include <cmath>
+#include <cstring>
 
 #define LMP_NEED_SPICA_FIND_LJ_TYPE 1
 #include "lj_spica_common.h"
@@ -37,7 +36,9 @@ using namespace LJSPICAParms;
 
 /* ---------------------------------------------------------------------- */
 
-PairLJSPICA::PairLJSPICA(LAMMPS *lmp) : Pair(lmp)
+PairLJSPICA::PairLJSPICA(LAMMPS *lmp) :
+    Pair(lmp), lj_type(nullptr), cut(nullptr), epsilon(nullptr), sigma(nullptr), lj1(nullptr),
+    lj2(nullptr), lj3(nullptr), lj4(nullptr), offset(nullptr), rminsq(nullptr), emin(nullptr)
 {
   respa_enable = 0;
   single_enable = 1;
@@ -71,6 +72,7 @@ PairLJSPICA::~PairLJSPICA()
   }
 }
 
+// clang-format off
 /* ---------------------------------------------------------------------- */
 
 void PairLJSPICA::compute(int eflag, int vflag)